The two were dealt with very differently.

Aether: observations show lack of aether so we update the theory that makes aether unnecessary.

Dark matter: observations show lack of observable matter so we keep hunting for decades locating it. The aether analogue would have been to continue to look for dark aether. Dark matter is more like god of gaps. We can 'darkify' any theory that does not fit empirical evidence.

It's hard to tell now which leans more towards the more correct theory.