Most hotels will NOT let you check in without one of the people named on the booking being present. There are multiple reasons for this, which range from legal requirements (in some countries) through to fraud prevention (not just for the booking, but even things like frequent stayer programs).
However all is not lost. You can generally list more than one name on the room, and in particular where you've got a booking for 2 rooms you can normally provide additional names for the second room.
If booking.com does not let you provide these additional names, then you should contact the hotel directly and let them know the names of at least one of the people in the second room. Once their name is on the booking, they will be able to check-in without you being present.
English language in Japan will depend on the hotel. In any western-brand hotels you can guarantee that basically every public-facing staff member will have good to excellent English. If you are staying in a smaller local hotel then things may be different. In this case you may be better emailing so that they can direct your email to a staff member who can speak/read English.