Daubreeite and Daubreelite

... I was just wondering if such similarly named minerals are not making the mineralogical classification a bit problematic..?

Both are grandfathered - at those times there was no IMA and no commission rules on how to avoid similar names.

And wath about smithite-smythite and renierite-reinerite?

It's the same reason as above. Both are grandfathered.

Plenty of names have been changed recently - like hancockite (and several others), so other changes could be made too (although I'm not in favour of that).

Others:

lazulite/lazurite/azurite
parisite/arisite
millerite/milarite
alstonite/ralstonite
berthierine/berthierite (the one I dislike the most)

And in russian, Gallite and Halite are very similar.

But then, we've even seen confusion in published references between bentonite and benitoite, and those are quite different compared to other examples!