I guess they're not using direct-sound / direct-input. Is there any issues about (not) using them apart from the extra coding. 

More or less, this is an extra level of insulation against bad drivers.

OpenGL driver bad or not installed? Windows 7 OpenGL performance is terrible? Bug X, Y, Z in the driver? No long a killer or source of aggravation.

MH's wrapper version 1 took about 6 hours for me to add to another engine.

The final one requires maybe a good 10 minutes (sounds so hard to believe, yet true), the wrapper is written that well.

Really although I think what MH did is an incredible think for Quake, I think the implications of this really go a bit beyond Quake or at least could.

I am thinking that many non-Quake games that used the OpenGL 1.1 or OpenGL 1.2 API set could be nearly insta-converted to DirectX API (Direct3D).

I mean Quake uses a large set of OpenGL 2D functions and 3D functions.