I first encountered the pipes in tekkit smp 1.12.2 and learned that its a submodule in another module called ProjectRed Expansion, but installing that mod in 1.16.5 and above doesn't have any pipes.

Were they removed? if so, why, and will they ever return?

Pressure tubes were recently re-introduced in a 1.20 version. Smart tubes will return at some point, though not in the same way as they were before.