I've only stayed at one place that would not even give me my key back between 10 and 3. Most of the other places just wanted me to be out while the room was actually being cleaned. I often come back for a nap around mid-afternoon before heading out for the evening. As the man said, YMMV.

As a side note, the American-based chain of Comfort Hotels has many properties in major Japanese cities that are very reasonable, a cut above most true business hotels and never restrict you from your room. They are certainly not very atmospheric or "Japanese," but won't begrudge you an afternoon nap. In Kyoto and Osaka, the Hearton Hotels are very similar, but are another step up, with on-site restaurants.

JR