Have you seen the capsule hotel in Japan? Its about 2 m by 1m by 1.25 m. , a space enough to sleep. Will you consider renting or having that kind of accommodation?
They normally don't allow women in most capsule hotels anyway, and they don't sound too hot anyway, I won't be going in one while I'm over there anyway. There are heaps of all nighter places where you can snooze, watch movies or play on computers anyway.
If you have tattoos you can't do a lot of things in Japan like visit onsen (hot springs), public baths etc Mainly due to tattoos being associated with Yakuza.
Well onsen and public baths you get naked for...so they'd be able to tell. As for the hotels...not sure, maybe if the tattoo is visable, they will refuse you.
I'm sure you could get away with tattoos if you're Gaikokujin... they're not going to think you're in the yakuza if you don't look Japanese! I stayed in a capsule hotel when I was in Shikoku... it wasn't bad! It was cheap and there was a TV in there and a shelf and a radio and a mirror. Plus, it's an experience, isn't it?