This is addressed in at least one Pokédex entry; for Darumaka, in White, X and Omega Ruby:
Darumaka's droppings are hot, so people used to put them in their clothes to keep themselves warm.
There are a few Pokémon that don't have droppings, but I think they are the exception rather than the rule.
A dangerous Ultra Beast, it appears to be eating constantly, but for some reason its droppings have never been found.
This Pokémon consumes particles that contaminate the air. Instead of leaving droppings, it expels clean air.
The way that both the Guzzlord and Weezing entries are written, I'd feel confident to say that they are the exception rather than the rule, and most Pokémon do leave droppings - the fact that Guzzlord and Weezing don't is exceptional enough that it needed special mention in the Pokédex.