Two cents from a (relative) newbie:
I think its important to recognize and accept physical limitations, and the effects of ignoring them.
Physical discomfort-to an extent-is one thing. "no pain no gain".
At the same time, fatique, lightheadedness, any condition that prevents you from being aware and focused on what you are doing can be plain dangerous.
We do a lot of things in training that are potentially dangerous. Training in a state where physical limitations prevent you from being safe (ie not being able to respond quickly and alertly while doing ukemi) might not, imho, be the best idea.
Fatigue, lightheadedness, cramps, etc... are often signs that your body is trying to communicate something to you--heat exaustion, dehydration, etc...
Don't ignore your body's warnings just to get in a couple of extra reps.