If having some questionable aspects in the thesis - like not elaborated and rather simple theoretical models -, that did not influence the whole work and results, but might still arise the thought "Why didn't the student know/do better here?", can this have a negative influence when applying to some graduate school?
My recommendation is for the student to make it clear in the thesis that they know these are overly simple theoretical models. If the models don't significantly affect the main results, it is difficult to see how being honest can hurt. And trying to make it appear that the models are more significant than they actually are could definitely hurt.