I’ve recently fitted some Vittoria Hyper 32mm tyres to a touring bike which has SKS P35 mudguards, which are supposed to be for tyres up to 28mm width. To provide enough clearance for the tyres to fit, I had to raise the mudguard at the fork crown (the bracket has a slot rather than a round hole to allow this) and push the mudguard close to the limit of the available length of the stays (if you have not cut the stays down too much already, this might not be a problem).
There is now a degree of toe overlap, but it’s not been a problem for me (as usual with toe overlap, strike is only likely with very slow speed manoeuvres – that may be a bigger issue for you on a 29er riding off road than for me on a tourer riding on road and gravel tracks). The sides of the tyre are just visible when seated on the bike, so I expect that in heavy rain and on wet roads the mudguard will not stop water being flung from the sides of the tyre when riding at speed/downhill.
Based on my experience, I would say that it is likely that it is the distance across the stay brackets (and the extent to which you can push them to the limit of the stays to get them further from the tyre) that will determine the maximum tyre width you can get away with.
There is good clearance otherwise between the centre of the tyre and the mudguard, so I am not concerned about mud etc. on the main central tread causing the wheel to lock up. That said, the Hypers are smooth road tyres, not knobblies, and I’ve no intention of riding that bike off road in muddy conditions, even with the reassurance factor that the SKS Secuclips provide.
In other words, it’s not just a question of tyre width vs. mudguard width: the amount of clearance your frame and the mudguard stay lengths will allow is also key, as is the type of tyre.
