Lots of reasons. Originally in the 1990s and thereabouts, the availability of high amperage DCC equipment was scarce and manufacturers of DCC had little or no interest in three rail O gauge, a much smaller market than HO and N, as examples. Lionel developed TMCC to be compatible with the high amperage AC open frame motors used historically and currently (in the 1990s) in their three rail locos. MTH developed DCS for similar reasons apparently. MTH did include DCC in many of their PS3 (edited 
) locos beginning in the first part of the 21st century so they could operate on two rail O gauge layouts. Two rail O gauge is an even smaller niche market than three rail, so once again, DCC manufacturers had little incentive to develop products specifically for O gauge, two or three rail.
Since all of the current production of three rail locos have TMCC/Legacy/LionChief/Bluetooth or DCS (Protosound 3), there isn't much motivation to spend more money on DCC for most hobbyists, except for those who like to tinker with such things. No motivation on the part of hobbyists means a tiny market, at least at present.
