Those who are in favour of a brexit on the basis of regaining regulatory control might be surprised by the number of international regulatory bodies such as EASA (and the court of human rights) where the UK membership is completely independent of EU membership.
A more serious impact of a brexit could be the need for UK citizens to get a work visa to work in continental Europe. This could make it difficult for UK pilots to get jobs on the continent unless there is a shortage of suitably qualified pilots on the continent.
Also those already working on the continent may end up needing to apply for a work visa in order to keep their jobs (and this would apply to a whole range of jobs not just aviation).
Matthew