I've had loads of incall punts in hotels and very rarely had problems, that includes with many EE girls and some of them have provided some of the best punting experiences I've ever had. Don't be too quick to write off all EE girls working out of hotels based on one or two bad experiences.
The girls who continually tour around or only spend a week or two over here earning before going back to their home country are only going to stay in a hotel, so refusal to visit a hotel means you won't be seeing them. The usual rules apply to spotting scam / B&S profiles or likely shit punts of course and you'll find them in private flats as much as hotels.
Answering the OP, of course the hotel staff know exactly what is going on and providing everyone behaves themselves they will take no notice. Just walk through reception, locate the lift or stairs as quickly as possible and get to the correct floor. Key cards can be a pain but then the WG has to meet you outside the room and it is easier to walk away if she turns out to be a B&S munter.
If anything the hotel management have come to realise that decent WGs bring much needed income to their budget establishment. The problems with EE pimps, B&S scams etc are a different matter though. One hotel in my punting area was notorious but seems to have cleaned up its act, the shit profiles now seem to operate out of flats, making them harder to spot.
Years ago I'd never have considered punting in a hotel, the first time I was bricking it as I walked up to and through reception but now I prefer it and don't care about the staff knowing why I am there. No shame whatsoever