It sounds to me like Armin is doing what so many on the other side of the pond are doing :: trying to locate a family connection or branch. Only in reverse fashion from what we are often used to seeing (with the majority seeking connections TO Germany). It appears he has been quite diligent so far in determining an outline of this branch, but is hoping to fill in a few of the particulars ('secrets' as he puts it, to which we all have a weakness in this pastime). Not to worry Armin, you're in like-minded company! 
Being a working stiff, I don't have too much extra time to pursue individual specifics for listers, all the more so outside of the California area. For that reason, I simply try to offer the best advice I can in where (or how) one can pursue certain leads. Fortunately others on the list have a bit more elbow room, as well as the requisite online tools to proffer some very helpful "specifics".
As I read it, it appears our friend Armin is first seeking clarification on what a Ancestry.com (German) marriage descriptor might be indicating precisely. Those with a subscription to AC may be able to help clarify this reference a bit better.
Secondly (and Armin take note), dates as they are listed in the censuses may not be "dead-on" as we say, in fact quite often they are far from it. Always allow a certain "fudge-factor" (leeway) of at least a few years up or down from what you observe listed. One quickly comes to see that many of the particulars in the census returns amount to "approximations", and are not always highly accurate. These inaccuracies are true for many other records too, not just the census ones, since much of this data is being rendered by family members, and is therefore based on the limitations of their knowledge or recollections at the time. So Frederick J. may or may not have been born circa 1843 in New York, at least until additional supporting evidence can be uncovered (unless you have more).
In the 1860 census i cant find the WHOLE FAMILY!!! Frederick A. is now a boarder in Richmond Virginia, this time named F. H. Hattorf born in the Kingdom Hannover:-)))) without family!!!! He marries again 1861 in Richmond, Virginia.
Regarding Frederick A.'s solo appearance in 1860, he may have been divorced or separated from his first wife at this point, or his family (or certain members of it, particularly with his wife) could have been the victim(s) of an accident or illness or death (assuming your 1860 Richmond, Virginia information is sound). If that were the case, the children may have been placed in foster care along the way, or may have been reared under the roof of a different papa, amongst other possibilities.
Thats all but i have nothing about his old family in NY. One thing is sure there was a Frederick and a George Edward Hattorf in the 13th regiment of Artillery in 1862 fighting for the Union, and i am absolutely sure that this persons are the sons of Frederick A. (who was in the southern army) it looks like a little family tragedy.
Your linking of his (possible) sons to the Civil War may point to a family "tragedy" as you put it (hinting of differing familial views regarding that conflict), or it could just be that Frederick Sr. moved to Virginia (for whatever reason) and his sons, being raised in NY, had natural allegiances to the state and "side" they called home. Hard to say if a "tragedy" is involved here or not, no?
I'd also keep an open mind as to the certainty that these are his sons in the Union ranks. They may well have been, only this is a huge country with many similar or identical names occurring here, there and everywhere - then and now! Moreover, if his son Frederick was not born until 1850 or beyond (per the 1850 census), that would place him at age 15 (at best) during the last year of the war in 1865. Not a highly likely scenario for seeing action during the conflict (though theoretically possible I suppose). Or was Frederick Jr., "his first born son", indeed listed in that 1850 census? [??]
So is there still a possibility to find out more about Frederick A and his time in NY??? How many children did they realy have? Are there churchbooks like we have here in Germany?
There would definitely be a various records to be found in NY dating back to that time period, but every state in the USA is different in what kinds of records they kept (and keep). There is no easy answer here, all the more so if the family were residents of NY CITY versus NY state. A city as big as NYC plays by its own set of rules so to speak, as opposed to the outlying counties and cities that surround it. You could almost call it "specialized" research, perhaps more than any other city in America, being that it is the largest city - then and now - in the country. You will probably have to determine the borough or precinct the family resided in, as opposed to just the city "proper" (main), which would likely be too broad. There are actual research guides and books written just on the subject of doing family research in NYC. These could be looked into, or perhaps a local area genealogist in the NYC area could be consulted or enlisted. Hopefully someone on the list has done family research in that city, and will have more to offer.
Also NY city AND state may have had a few of their own individual censuses enumerated over the years, as opposed to the FEDERAL ones we all generally reference. That alone could offer additional possibilities. Try NY STATE / CITY CENSUSES in a good search engine. Certificates of death could also be sought, once enough supporting documentation is found. Likewise Civil War records on the sons from NARA (National Archives). It goes on and on from there. Depends on how much time and/or money you want to spend in the end I suppose (as in everything else).
Now don't keep us in suspense Armin. Many will be curious as to your connection here. Is it a case of the Deutschlander seeking the Amerikaners, much to our naive surprise? You mean... it can work both ways? <lol>
Now if that's the case, we are unfortunately coming up a bit short regarding Jan Timphaus's request [February�1] for more info or possible leads on the GERHARD WINGERBERG�family who came to the USA in 1875 from Westerholte (though Barb may have found a newspaper obit), with daughters Elisabeth and Wilhelmine. Also Baerbel's request [January�29] for perspective leads on HEINRICH BEHRENS from Luttum, who may have emigrated to America and had two daughters, Gisela Charlotte Behrens and Ingrid Erika Behrens. Maybe someone with the right tools could give these a shot also (Barbara is working overtime as it is, with Gale pulling up the rear).
For a start, both of our German side requesters could subscribe to Ancestry.com for a free 2 week trial if possessing a sufficient command of English, and peruse the gamut of records found there. Sounds like Armin may already have.
Best of luck. Jb