Odd glitch with transparent textures
I see you have a space in the map name. IIRC that may cause these kinds of problems. The game doesn't always handle spaces correctly, and since the cube maps are stored in a "virtual" folder with the same name as the map, it may not be able to find them.
Try renaming it to "hotel_aperture.vmf" and see if that fixes it.
(I can't build it because it's missing some instances.)
Other Portal 2 maps: Medusa Glare
Portal 1 maps: Try Anything Twice | Manic Mechanic
That is very strange. I've never encountered this particular glitch, but about 80% of the time any PTI map I export to Hammer won't have any cubemaps.
Think of all the things we learned
For the people who are still alive
I'll try that HMW, thanks
Also, I have been advised that it may help appearance to put cubemaps over other reflective surfaces like glass and water, is that the case?
Amazing, it worked. You have my sincere gratitude HMW, you have saved me enormous headache. Thank you!
Glad to have helped! 
It's a good idea to place additional cube maps near reflective surfaces, but don't overdo it. If you have too many, you will notice more sudden changes in the reflection on e.g. cubes and the portal gun model. Also, each cube map takes up some extra space in the bsp file.
Other Portal 2 maps: Medusa Glare
Portal 1 maps: Try Anything Twice | Manic Mechanic
I've taken that onboard and placed some additional cubemaps inside the map, only one per surfact