I asked REL about bird strikes and got this back
Yes, we have considered FOD but do not think it’s a problem. A first
generation space plane like Skylon will only be designed for 200 flights or
so, however bird strike occurs at roughly 10^-5 for civil airliners (from
memory) so the probability of a strike over the vehicle life is quite small.
Nevertheless FOD and birds will pass axially along the intake duct and strike
the bypass burners rather than the precooler which is tucked away inside.
Since the bypass system is not running for takeoff this will result in a
mission abort rather than loss of vehicle