Why formulate drugs as HCl salts when HCl is in stomach acid?
Another reason is that many drugs which are conjugated to hydrochloride salts is they are amines, and amines by themselves often stink. So people might be turned off from taking drugs that smell terrible (fishy). 

Now, note that even though a label might say something such as "fexofenadine HCl" that doesn't mean there is HCl in the drug. Fexofenadine is an amine, and amines are somewhat basic - and more than basic enough for a strong acid such as HCl to completely protonate. 

So if this is what you had in mind for the structure of fexofenadine, it isn't the most correct structure:



This would be a much better structure. The nitrogen in the ring has been protonated and it now bears a positive formal charge. Chloride ion is the counter ion.