There are for and against, its an ongoing debate.
My view is this, I contributed to an earlier thread on this very subject not too long ago.
Rays will live on both substrate or plain glass, they will reproduce using both methods also.....does this mean both methods provide a happy existence? I believe not!! Rays are extremely intelligent fish which require some sort of stimulation to be as happy as they can be kept under captive conditions for our pleasure, burying when they feel the need and blowing through the substrate as they so often do are mannerisms we should not as aquarist deprive them of, these are not trophies that should be kept in a plain glass box, yes the rays look great this way and photograph beautifully but for me its a boring life for both the ray and aquarist alike. I tried it for a little while not long ago after using substrate for more years than I care to remember...I soon changed back to substrate.
An interesting observation during this 6 months or so was my female P12 Henlei's bizarre behaviour. I noticed her spinning on the spot at regular intervals, these intervals became more frequent to the point she was doing it as much as she wasn't, this had never happened to any of the other rays I might add but it was becoming disturbing for me to enter the ray room as this was the first thing I went to look for rather than enjoying the fish. I always had my doubts about bare bottom but this finally answered the question you are asking now...for me anyway! I eventually added the substrate back to the tank\tanks and I got the result I was looking for, not straight away, it took several weeks for her to resume normal behaviour, this was many months ago and I am pleased to say she is back to normal working the substrate and generally looking great, in fact she is due to give birth anytime.
I use glass bottom on both new imports and new born pups for a short period, just while they are feeding satisfactory.
Please note this is my personal view. Many aquarists on here use glass bottom to good effect and are very happy to do so and their rays\fish look fantastic.