@Valgys A possible compromise: have the item clear only specific things like common minable blocks, and leave the other stuff alone.
The selector for item clearing is /kill @e[type=item], I don't believe you can actually select just certain items, I will have to test around.
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Response to the Suggestion:
My add to this is that dropped items pile up quickly. Lots of entities slow up the TPS and can eventually make the server unplayable.
The solution you are looking for in the long run is adding a /title as well as a chat message. Titles come up even with chat disabled and you really can't miss them. If you don't know what a title is, it is the image shown below.

Good Day,
~Jams__
(Ignore the sidebar in the image. I forgot to remove it when I took it, in fact, ignore everything but the title. I just did it where I was.)