- In general, no, you cannot ask for a different time for dinner/breakfast. As the chefs, kitchen staff and room servers need to wash up and go home for the day, rest, or start getting ingredients for the next meal, they have their fixed time slots.
- Lockdown: Um, if you are talking about real "ryokans" (not the inexpensive, Japanese style budget places), when they lock down, the head staff members are asleep, and the room servers are either asleep or gone home. It's not like a modern hotel where you've got a janitor or security guard up all night. You'd better return before that.
- Nap in the afternoon: be sure to ask up front if it's OK you use the room during the day (meaning after the regular check-out time). Once again, after the regular check-out time, which is normally 10 or 11, the staff clean up the vacated rooms, if they serve lunch in their restaurant they might be busy with that, etc., that they are not really assuming that anyone uses the room during the day.
If they say no problem, you could even set up the futon yourself, but if you are staying at a place where your meal is served in-room, that would give the staff extra work of putting them back up again before serving your dinner.
- Apart from big cities, yes, night life shut down early. Or, even in big cities, bars may be open till 3 in the morning, but regular restaurants stop taking orders around... 22:30 or so. People (residents) need to think about getting home too. Trains don't run around the clock.
About ryokan, generally speaking, though I am Japanese living in Japan, I find the protocols at ryokan too stiff and inflexible at times that I prefer to stay in western hotels, or at least ryokans where they serve meals in their restaurants, not in-room.