Ah, love hotels. What a great idea! IMHO Love Hotels run a close second to the light bulb as the greatest idea ever!
Well, the ones I use are mainly in Shibuya, on Love Hotel Hill. But there are loads.
Entry offers a variety of possibilities.
Almost always there is a large panel with photos of the rooms in the entrance area. The ones available are illuminated. You select your room by pressing a button near the picture. Then you walk over to the reception counter. Sometimes there is a member of staff at the reception counter, usually sitting somewhere behind a closed blind, but occasionally in plain sight. You (or more often your Japanese date) tell the staff member the number of hours you want to stay, pay the required fee in cash (around 3000-5000 Yen for 2 hours), and are given your key. Then you and your date head up to the room, enjoy your time, and return the key upon leaving.
But some Love Hotels offer total discretion. There is no one on duty in reception. Instead, large touch panels or screens enable you to choose your room. There is no key either. You simply go to your selected room number. Above the door a light is flashing, indicating the door is unlocked for you to enter. Once inside, you lock the door and your time begins. After your fun, you pay via a machine in the room which accepts your cash and gives you your change before clicking the door unlocked for you to leave.
I usually see girls in the afternoons too, and have never had a problem finding a Love Hotel. I think some in Shibuya may stay open 24/7. During the earthquake I was stranded in Tokyo and spent the night in a Love Hotel in Nippori (alone, unfortunately), but that may have been a special case. Anyway, there are loads to choose from in Shibuya open from noon, possibly earlier. So you shouldn't have any problem finding a place. No credit cards are required, so no need to hand over any personal details. You don't sign in either. Discretion is the rule. And I've never had any issues with the rooms themselves. They are always clean, with showers, sometimes jacuzzi baths, freshly made beds, widescreen TVs showing porn or standard programs, hairdryers, towels, bathrobes, toiletries, and yes, condoms!
Here's a link for Love Hotel Hill:
http://www.lonelyplanet.com/japan/tokyo/sights/neighbourhood/love-hotel-hill
Have fun!