Lying about a criminal record on a school application is risky, though in some circumstances more risky than others. I've spent time working for the admissions office at a major university. I know that at UT at Austin, not every appliant was checked versus any sort of criminal history report, but that varied widely according to which programs a student was applying to and whether the student was an undergraduate or graduate applicant. In programs where the vetting process and admissions requirements are somewhat higher, the probability of a check naturally grew. Graduate applicants to both the college of engineering and the college of natural sciences were always checked because those students so often worked in labs and on projects of such a sensitive nature.
There are a few factors to consider. How large is the university? The larger the university, the less likely that your criminal history will be checked. Trust, if every student at a university the size of UT was subjected to a criminal history review, the costs would be stupifying. How "sensitive" is the program to which you're applying? If chances are the department at the university in question does a lot of corporate or government contracting, the greater the probability that a check would be required. Finally, does the state in which your university stands require a check by law? I could swear that a couple of western states actually do require a check by law. I also know that several states do require a background check in order to qualify for financial aid.
In summary, my experience has been that yes, backgrounds were checked, but the circumstances varied. My recommendation is that you be honest. If there are any questions that arise, be prepared to be open and completely truthful. An honest applicant stands a much better chance at admission under any circumstance than one who chooses to omit any piece of information.
Good luck. I hope I've helped a bit.