To answer the question at hand, "Why don't more Federation Ships have center Warp?" is simple, yet complex.
If you are coming from a Trek canon point of view, then the "Gene says so" explaination above should simply answer the question.
However, I think you are asking from an SFB/SFC point of view, so I will answer as best I can.
The F-CC and F-CC+ were the Command Cruisers of their time. The F-CB is/was(/will be?) a Heavy Command Cruiser, a replacement. Throw in that SFB Fed ships can separate saucers, and mix it up with the "c-warp durability", also above, and you get a survivable piece of a command cruiser. Saucer sep's are a last ditch effort to keep the ship in game (or action), usually used after the ship takes catestrophic damage; however there are exceptions to the rules. Until the saucer is free and clear of the rest of the ship, the c-warp is power only, it can not be used for movement; this applies to those (few) that have the smaller (2 box) c-warp. DN's are another story. This is also true of the Klingon penal cruisers and the C-7 class hull.
You are correct in assuming that the F-DN's are essentially F-CC's with a touch more gusto (until, of course, you follow the DN with DN+, DNG, DNH, etc...). The c-warp here is just as important for movement as it is for weapons, et al (yes, from a non-SFB standpoint, it does take the power generated from the reactor and converts it to a warp field). Unlike its smaller counterparts, the c-warp on DN's is fully functional with the ship complete or separated.
It comes down to balance and durability. There is a lot of fed ships that have c-warp, and I'd say that at least 80% have a standard L/R-warp pair as well. I don't have any paperwork in front of me to quote specific ships, but I know that there is a lot. Of those that have only c-warp, well, that's all that they have. Nothing more; nothing to throw off the balance; a single nacelle slung below (or above). When a ship has just c-warp, any hit scored on L or R-warp does damage to the warp engine. There is no "cushion" of another nacelle or two to mitigate the damage.
Take the F-DD, 15 box C-warp. That means that 15 R/L/C warp hits and she's OOC. On the F-CB, it might pan out as 7-L, 7-R and 1-C for the same 15. F-DN might look similar.
I don't know, I guess I rambled on, but the short answer is balance and durability.
Of course, if you are just asking why more Fed ship models don't have c-warp... well, I just don't know that one...
Czar "I think I answered nothing" Mohab