I'm not too informed on this topic - but I'm just trying to help:
They can do mods/plugins together, but they need special software like Sponge and Cauldron. The reason they don't add it is that most of these softwares are discontinued, not fully released, or just not popular enough. Cauldron was discontinued, and Sponge is in Beta and also a very small software (at the time this is being written). Personally, I would like to see Sponge implemented, since I would like to set up a modded server with plugins, but at the end of the day it's up to the staff at Aternos.
I hope this helped,
mikey0619