The item duplication 'feature' of Terraria has been in the game for 6 years - it isn't going to be patched out. Items have no intrinsic value inside or outside of the game, and no one can tell a duped item from a 'legit' one. Trading of items is only for entertainment purposes - some people just like to trade things.
The Coin Gun pretty much assumes that you're going to dupe/trade/invedit (PC only) coins to make it viable as a go-to weapon. The devs are well aware of this. There are other guns as good or better, so it's really a personal choice to use it and to use whatever method to obtain ammunition.
Other 'glitches' - like liquid duplication and hoiks - have become integral to the game experience, and as long as they don't cause other problems are probably going to remain.
The devs are aware of most if not all of the glitches, and you can always report them in the
Console Bugs section.