How common is toe overlap on 29" wheel bikes? Also, is there a way to fix the overlap by say replacing the shocks for some with more travel? Lastly, is toe overlap a major issue on a mountain bike?
It is known some people moving to 29er's have issues with tow overlap, especially on small frames. I know when I am not using cleats, I sometimes get a bit of toe strike, less so now, but initially it was happening regularly.
Best not to try and 'fix' the overlap - the bike geometry will be negatively affected unless extreme care is taken. Its not a major issue, you get used to having to keep your feet back (where they should be for efficient riding) Clip less pedals solve the problem completely.
There is a reason the industry quickly moved to 650b. One take is one size does not fit all as the failed 29 experiment shows. The other (cynical one) is the industry needed a reason to sell more bikes, so they came up with 29er as the new "must have" for a couple of seasons then introduced the 650b and said "this one is much better again", knowing all along 650b was a better "one size for all" size.....
I don't know how common it is. I can tell you that it's not as big a problem as you would expect.
Toe overlap only comes into play when you're making very sharp turns at low speed. Hitting your toe on the front tire would be dangerous at high speed - but at low speed, it's just annoying. And it doesn't even happen that often.
I have a 46cm gravel bike with 170mm crank arms (it's a Surly Cross Check, it's approximately equivalent to a 50cm road bike ). Although it isn't a MTB, it's still a 29er (700c = 29er with narrower tires). Indeed, toe overlaps are issues for me, although they are more like annoyance.
Toe overlaps mostly happen when I stop at a red light, or sudden strong braking (almost completely stop) with a sharp turn. However, when I ride the bike in trails with twisty turns, at a reasonable speed, toe overlaps have never occurred.
I think toe overlaps don't affect the riding performance. At first, it's quite annoying but it's not the end of the world. After a while, I'm used to it and I don't plan to modify my bike.
edit: Recently I've been trying a lot of things on my bike, here's what I can tell from my experience:
Go for thinner tires, I used 700x40 tires and toe overlaps happened more often. Afterwards, switching to 700x35 tires reduces the occurrence of the problem. Depending of the tires, 5mm tire width difference is very noticeable, since the diameter of the fully inflated tires can be significantly reduced, so the distance between the pedal axle to the tire surface is increased.
Use clipless pedals. This might not help depending the pedalling habit while using platform pedals. When I used platform pedals, my foot position was already around the ball of the foot, so after switching to clipless I do not feel any difference. However, clipless pedals give some kind of predictability since my foot position does not change so I can guess/predict when the toe overlaps will likely to occur and I rotate the pedals backward to avoid them.