So, historically, because of various sticky statements that we can write down that make no sense (Russell's paradox, Cantor paradox, etc), we have felt a need to formally justify our use of all symbols in mathematical statements, to give them well-defined, formal meanings, as if they were elements of computer programs.
Numbers and sets provide unique challenges if we try to do this, because they are /integral to the very basic concepts of proof itself/.
The way that you resolve these challenges is a formal set theory, wherein you get statements like {}=0. Think of it like "0" is defined as {} for our purposes - we are starting with a world where the symbol '0' has no meaning, and proceeding onwards to do... the entire rest of mathematics, with nothing a formal set of rules and some axioms (statements assumed 'true').
The construction of the natural numbers you give is by no means the only one possible! So the statement "0 = {}" is not a universal, given, derivable, etc... thing. It is just one way of reconciling the concepts of numbers and sets with regard to a formal system of logic where we can avoid some of the "nonsense statements" that have caused logicians and mathematicians grief in the past. There are others! Studying the extends to which these models are equivalent / apply to each other in the presence of various sets of axioms is a discipline of logic with a rich body of literature.
You really needn't worry about it on some "fundamental" or intuitionistic level, unless you are interested in that sort of logic.
[edit - I don't have enough "reputation" to comment on Frunobulax's post below (bombs won't stop him; we're going to have to use NUCLEAR FORCE! :) ), but breifly, yes I mostly agree with what he is saying - the development of the formalism was/is not a "tangential" activity - there is no good reason to believe people and people are talking about the same, consistent, mathematics without it, instead of some kind of pre-Babel situation!
The real numbers are somewhat different than the natural numbers however, as these are not so intimately related to the ideas of proof (ie. the metalogic for all of the mathematics including the domain of reals can be expressed without reals for most every non-exotic/non-contrived model, etc) This touches on the "non-belief" in real numbers... although I don't think anyone doesn't believe in /countably infinite/ sets, as again there are certain proofs that require rather... complex... proof systems without them.
This is admittedly a sort of a nitpick, however...]