I actually did hear the above - that facial hair helps build rapport with locals - to be true. Integration and interface are two different things. While SEALs might not work closely or integrate with indigenous peoples, their job could still require interfacing, formal or informal communication, with locals in a number of capacities. I understood beards signal a mature man worthy of respect in some middle-eastern cultures - thus, more likely to garner honest and substantial input from members of the community.
The blending element is also pertinent. So facial hair can serve multiple functions, as with non-standard or theater-specific (shemagh) articles of clothing.
Beards are also said to interfere with gas mask seal. I'm not sure if anyone can chime in as to how concerned operators are with gas attacks, but this is part of the reason given for shaving with "regular" servicemen.
I would not attribute beards to nastiness or poor maintenance of hygeine. Guys at hellhole FOBs still manage to keep with the grooming standards. Friend of mine has pictures of when he had to wear trousers caked in human poop for three days straight - like many, he got smelly, but he's not wearing any stubble. I'm not saying appearance standards are enforced everywhere or aggressively on deployment, but it's certainly not like they can't or won't shave.