roadbloc, I think you don't understand how the move to a retina display is likely to happen. With the iPhone4 retina display existing games worked without being modified. This was possible because they were rendered at the old 3GS resolution and then upscaled. To take advantage of the extra resolution of the display Apps had to rewritten but most of the existing games worked fine and no looked no worse than they did before.
Given that Doom and Quake both have low res textures and graphics by today's standard I don't really see much benefit in a retina display for them. As to why there isn't iPad native versions I think it comes down to id not being interested. There is an iPhone version of Doom which works fairly well on an iPad but I guess id would prefer to push new games (i.e. Rage) instead of porting old games.
Both the Doom and Quake engines have been open sourced so someone else could do the work of porting the engines to the iPad. This is the big factor in why these games have been ported to virtually every platform out there. However the content of the games (levels, models, textures, sounds etc.) has not been opened and cannot be legally distributed by anyone except id. This means that a third party can't put a full Quake game into the App store and I also doubt that Apple would allow an App that asked the user to provide there own data files.