Is there a minimum height regulation for emt conduit in a garage?
There is no height requirement in NEC Article 358.12, "Uses not permitted" so long as the run meets the other requirements. There is also no height requirement for task lighting over a work area. The only "standard" height for work areas I have ever heard of was 30" above a work area. I assume this is to allow you to put things on the work area and provide adequate head clearance. It would be practical to provide some sort of protection from any glass breakage such as a wraparound fixture or lamp protectors.

If you would like to review NEC requirements on fixtures go to Article 410.