Why was this removed? Could've been provided via the resourcepack.

Re the /tardis egg command, there must be a problem at your end. I wouldn't have pushed a commit without testing it first, and I have zero issues on my server.
Have you updated the resource pack?
Make sure the Minecraft client music volume is not set to 0 as the theme sounds are set to the music category

I can change the functionality of the delay when just using /tardis egg without any further command arguments (which defaults to choosing a random theme from the three options - where the randomness is determined by the Minecraft client not the plugin so I don't know which one it is going to choose...), but how often are you actually going to be using the command regularly?

Not too often.

The code was removed as it didn't work - that doesn't mean to say that it won't added back into the plugin in some other form, but I wasn't all that happy with how the theme sounded anyway.

How do you add a .NBS file to a resource pack?
Do you mean as a datapack - which is possible, but won't make it sound any better.
Or do you mean adding an OGG file to the resource pack and playing that instead of using noteblocks?

Yes, an .ogg file.

I'd like that better (the being in a resource pack), plus could make it sound better and would be less reliant on the server running properly, and much easier to maintain.

Alright, cool.

Though, how and when/where does it play? Or is it meant to be used for roleplay.

There is a random 3% chance it will play if the (Doctor Who) quotes player prefs is on and you are entering the TARDIS.
Otherwise you use the command /tardis egg [SIXTY_THREE|ZERO_FIVE|TWENTY_TWENTY|RANDOM]

Update your TARDIS Resource Pack