Should I place air holes in my custom MacBook Pro case? I'm fabricating a plexiglass case just like this to snugly fit my new MacBook Pro. I'll slide the laptop inside whenever I'm traveling for safety reasons. 

It'll only be accessible from the right side. Should I place air holes in the back if it's going to be on whilst the lid is closed?
Yes, you definitely do not want to block any vents - no matter if the lid is closed or not.

You can read Apple's instructions on not blocking vents here:

https://support.apple.com/en-gb/HT202179

Note that there are vents both along the side and on the back of the MacBook Pro. Don't block any of them.