I always thought it ought to take an absolute majority (not counting vacant seats of course) to pass anything (why not?), that would get around the problem.
You’re assuming that you’ll always have perfect attendance, which won’t be the case. I wouldn’t want one of Trump’s judicial nominees to get 49 votes for and 44 against and to have the nomination defeated. Besides, Congress always has permitted bills and nominations to be aporoved by majority of those voting, not of total membership.