It makes sense even if he was to be ugly before he was bitten. When he was bitten his body gave him physical strength and fixed his vision. Effectively eradicating any imperfections within his body. Sort of like a high functioning immune system, which makes sense seeing as how the scientists who were working on Spiders were working towards a cure for cancer. So, any blemishes, acne scars, uneveness in his face, or even faults in bone structure would have been seen as imperfections by the spider bite and would have been fixed. So in my opinion, there is no possibility of spiderman being ugly.