Yes they do. AF accuracy depends on all the mechanical parts lined up properly and through use, wear and tear happens in the movable parts and degrades the AF accuracy gradually.
Main mirror has two hinges connected to the mirror box, two stoppers to rest on.
AF submirror has two hinges connected to the main mirros, one or two stoppers to rest on.
For each picture taken the mirrors have to swing up and down in rapid motions. The hinges can get worn, creates play. The stoppers can be knocked out of position. Both will affect the mirrors' position and angle.
When that happens, if the mirror box has means of adjustments, then can be adjusted to gain back some performance, otherwise nothing you can do about it unless replace the entire mirror box assembly.
Electrical adjustments can also be done but when doing that on a worn mechanical system, it's just a band-aid solution. Sooner it will be out again.
And if you have to ask, I know what I'm talking about (picture showing main mirror hinge position adjuster):
I've completely dismantled my 1D Mark III to fix a mirror problem. Whole set of images: http://funkyrider.minus.com/mblciPXA9phttp://funkyrider.minus.com/mbnjGRNB2x
Even top of the line 1D do get out of focus by various reasons. However they are all metal on the construction and are fully adjustable, which makes the cost of maintenance relatively low. You can fix instead of replace most of the time.