Hello Mav, welcome to eforum.xxx!
If you stick with the normal agencies, such as the ones you mentioned, you should be fine. All three of those have really good reputations in that regard.
What you don't want to do is invite unknowns, such as people from Craigslist or other sites that don't have a known reputation. To my knowledge, there havenโt been any incidents that were considered "major".
There are a few things to consider: If you don't live by yourself and have housemates, in some cases they won't send a girl to your apartment. That's mainly for the safety of the girl that would be coming. If you are concerned with the girl stealing something, I really don't think that's an issue in Japan.
Just be respectful to the girl that comes to see you, don't offer her any alcohol or or anything she could deem to be risky. Have fresh, clean towels available and don't make her feel restricted. Don't be offended if she doesn't use or take something that you offer.
Maybe this explanation was a little excessive, but these are just common things when you have someone visiting your place. If you have more specific questions, let us know.