I have a question about pysical conditions and if playing instruments can be the influence/cause of it.

I recently discovered I suffer from pectus excavatum, though it's a very mild case in comparison to pictures posted on health and medical sites. I first noticed I had it while watching a medical programme on tv, and heard it can affect breathing (i'm a flute player) so I went to have it checked out. The doctor didnt really say much about it except that it's quite common, that it isn't serious looking, and that it was probably because of the fact i've have been playing woodwind instruments since i as 12 while bones are still growing.

I thought this was very strange because lots of people start wind instruments around that age, and younger. Can anyone confirm that playing a wind instrument can have such an effect on bone development?

Good news is that breathing isn't affected and it hasn't held me back anyway in my playing (6 years on I'm now doing BMus with flute as principal study).

It can be very difficult to work out cause and effect - but I would say that playing wind, and especially relatively low-pressure wind instruments would not cause pectus excavatum. The main medical causes of it (and it does happen quite naturally too - it's a strong trait in my family, and I'm the only wind player) are conditions which cause difficulty with breathing in rather than out - the diaphragm has to pull on the rib cage when filling the lungs with air. It is therefore more commonly seen in kids who have had moderately severe asthma from very small, for instance.
I am aware of one instance in which starting to play early actually brings anatomical benefits - violinists who start very young will often develop a different arrangement of the flexor tendon sheaths in their left hands, which helps with more independent finger movements - normally the middle, ring and little fingers share a tendon sleeve, but in people who use their fingers in the way a violinist has to, these fingers are more likely to have individual tendon sleeves. I can't remember all the details of this now, and it may well be that pianists starting young also benefit in this way.