The other answers tend to treat this from the perspective of ZFC, a specific way of formalizing the ideas behind set theory; below I give a more informal approach, which has the benefit of applying to set theories other than ZFC.
they are well-defined collections of mathematical objects
The emptyset is a well-defined collection of mathematical objects - it's certainly well-defined, and every thing in the emptyset is a mathematical object! (Every thing in the emptyset is also a purple unicorn, but that's fine - there's no rule saying "a set has to have something which isn't a purple unicorn.")
Ultimately, this comes down to the question, "What is a collection?"
This ultimately comes down to relevance: for any mathematical object, there are questions about it which simply don't make sense. E.g. is $17$ blue? Informally, a statement like "A set is a collection" tells us what a set is by telling us what it does: the only meaningful questions you can ask of sets are those which revolve around membership ("Is $x$ in $A$?" "Does $A$ have at least three elements?" etc.). This is also the motivation behind the Axiom of Extensionality, which states that two sets with the same elements are the same.
Now it should be clear that there's no problem with a set being empty: that just means that whenever I ask "Is $x$ in this set?," the answer I get back is "no."
Now it takes some work to make everything I've said above precise, but the intuitive meaning of it should be clear, and hopefully it's somewhat persuasive. Personally I would say that this kind of "limiting meaningfulness" approach is actually of fundamental philosophical importance to mathematics, and there is a philosophical debate around this point, but that's going far afield.