I use a Camelbak all the time, road and mtb use.

When it gets muddy on a mtb ride I throw the bag (not the bladder!) in the washing machine, looks nice and new again in no time!

I can understand your concerns re germs and bugs lurking in the bag and pipe though. I use steriliser tablets, the ones that can be used to clean baby bottles. When I get back from a ride I just wash it all through with clean water and then soak the lot in the sink with water that has been mixed with the steriliser tablets (or liquid, we use Milton here in the UK) and then let it dry naturally. No aftertaste, just nice and clean.

Job done