Is it ill-advised to make a cover for your thesis in STEM? I handed in my undergraduate thesis in mathematics and since I had extra time due to COVID-19 lockdown, I had made a cover drawing for it that I included. I've never seen a thesis with a cover in the STEM field before. 

Was it a bad decision on my part? Will it look like kowtowing/bootlicking my supervising professor for a better grade? I believe my work was pretty good on its own and I'm afraid I have ruined it with what was intended as a personal touch that I really wanted to add.
It does not matter.

It used to be that theses were printed on paper.  In those days, they had standard covers so they would all look the same when placed on a shelf in the library.  

Today nobody cares about a digital cover.

Be prepared to provide a copy without the cover if someone asks for it.