Unless there is a special exhibition (and even then), lines are not a problem. I even went to the Nara National Museum while the Shosoin collection (8th century Silk Road artifacts stored in an 8th century wooden warehouse and brought out once a year in October) was on display, and there were no lines.

The only time I even heard of lines was in the 1970s, a few years after Japan and China opened diplomatic relations, and China sent an exhibit to Tokyo for the first time.