when i was backpacking hokkaido, i met few japanese w/ tattoos inside onsens.
either thats their territory, or the stereotypes no longer as strong.

as long they dont cause any ruckus, other non-tattood japanese pretty much just carry one w/ their stuff.

if you got tattoo, you can just ask the counter 'tattoo daijobu desuka?'+ buat muke sposen.
then if allowed to go in, just duduk at certain corner. most likely ppl wont notice ur tattoo