Actually, that's a really good question. You'd really have to ask at the hotel to find out.
I've found out about hotel's 'love tax' as my partner is Japanese but lives with his family. I was there a couple of years ago when his mum died. All I wanted was to be able to stay somewhere where he would be able to come and join me occasionally (naturally, it wasn't appropriate to go to his house). It ended up being a REAL problem, but I was there for a month so the way round it was different - I found a room in a house to rent.

My advice is to find somewhere where you can have a semi-double and say that you are paying for two people, but you are not sure when your partner will be able to join you. Both the hotels SNA767 recommended should be able to do that for the same kind of cost you mentioned originally. If you're still having problems then www.hotel-parkinn.com near Shinjuku San chome should be able to help - they have no curfew and the guys in reception are pretty nice - but SO overworked, they never seem to sleep (more info here: http://flyertalk.com/forum/showthrea...96#post3623196)
a small double here is 8,100 - I never had to pay the 500yen for the TV, but I can't guarantee you won't. The room also had an empty fridge, which is useful in the summer.
As for the AMEX/VISA/whatever, it's a problem all over Tokyo about whether the machines will accept them. Maybe it's different with American cards, but I've had awful problems with UK ones, and so have people I know from here (UK) who are gold/platinum/diamond/ruby encrusted card holders. All I'm saying is be prepared in case your card doesn't work, that's all - have at least 1 night ready in cash to pre-pay if you have to. (If you do get stuck and Citibank won't give you cash, try the Post Office's machines -green yubinkyoku, symbol looks like an irish clover leaf- they've proved virtually failsafe for me, apart from at New Years when they were closed for 3 days ).