Running a /search is quite expensive, so we do cap the returns at 2000. Note that this limit is not contractual, and subject to change (it has been pretty stable for a while, but we're seeing thousands of new posts a day... we may encounter a tipping point in the future).
In this case, if you want all questions tagged matlab this is a better query. If you're not using nottagged or intitle then /search is probably bad fit for you.