I rarely book hotels in Japan directly. When I use an overseas OTA (even though I live here), I always check the single and double rates they're often the same but not always, so I check both. If they're the same, I always book a double to get more towels, etc. (particularly in summer when I'll want to shower multiple times a day). Regardless, be mindful of bed sizes. They're often quite small.

The only issue that comes up with that is that *some* on-site local taxes and fees (such as for using the public bath) can be based on the number of people. At one hotel I like to stay at in Kyoto, this is an issue but when I say it's just me, they've so far removed the extra charge for the second non-existent person.