as a patron the bar would rather you spend your money on booze anyway so protesting the merch tax by not buying anything except more beer is advantageous to the club
the only time you can challenge that is when, as a band you are drawing enough to have any leverage with the club. and, yes, the merch fees are often in the contracts.
and, A lot of bigger venues will have someone do an independent count of the merch and totals to make sure it's all on the level so there is little wiggle room for the band to cheat on the figures.
yes! yes they can and do, often. When it's $35 for a t-shirt, that's why. I've gotten so much flak from people about this kind of shit without people knowing just how much is taken off the top..
there is also management taking their cut.. %15, plus paying merch staff 5-10% and promoters/venues taking 10-20% all from the merch totals..
it adds up