What does it mean "the rate is for 2 guests" does it mean multiply by 2 the advertised hotel rate?
It means the $ value shown is for two guests (that is two people are allowed in the room).
Often hotels apply a surcharge if extra people are wanting to share a room.
However, since you've not specified the site, I'll also mention that sometimes it means you can't have less. For example, a twin dorm in a hostel often requires you book both beds. So you can't have less than two people in the booking - ie the booking is for the whole room, and the 'rate is for 2 guests', in this case.
In Japan, unlike most of the world, you pay per person, not per room, for most hotels.
So for instance, if I travel alone on business to a hotel, it will be ¥6,000/night/person (assuming two guests). If I actually try to reserve it for one person, it will likely be a little bit more (maybe ¥6,500/night) for the exact same room. This does not make sense at all, but it's the way the system works.
Take this search:
The rate shown is per person (4,000円〜/１名), but assumes double occupancy. If you actually go through and change the number of guests to one (you need to sign up for an account and read some Japanese) you will end up getting a somewhat different price most of the time.