Why is there a two hour time limit on a morph? Is there anything in canon that explains why?
It is explained, although not in great detail.
Morphing is performed using an "Escafil device" or "Andalite morphing cube". This is a device made by a people known as the "Andalites".
We're never told how and why this works, or why there is such a limitation: it is simply a limitation of the technology. I believe there is a reference at one stage to Andelite scientists attempting to improve the technology.
It appears, therefore, to be something akin to a battery life or capacitor capacity.