Not many... I asked the same question in those Talks organised by Shatin secondary schools. Most of them (should say Band 1 schools) do NOT have proper school swimming team (I mean those practise several times a week under the school coach).
Those schools sending students to attend the inter-school swimming competition may not have proper school swimming team thoughout the school year. They may gather those interested students to swim several times before the competition, or even without any practise as they assume that their students have their own practises under the guidance of private swimming club/team/coach.
I read from Baptist Lui Ming Choi's website and guess it may have its school swimming team but not sure how frequent of the practices.
http://www.hkssf-nt.org.hk/district/sec/02sw/Swim/record.pdf。 this is the swimming competition result 沙田及西貢區 last year. So you can find those school join 學界游泳比賽。