Can't say I have seen these pipes, but there is a pipe on the West Cove beach. My guess they were for sewage from the base. There were pretty extensive coastal batteries up there during WWII along with the anti-submarine nets. Back in the day if you couldn't see the turds floating around, you were considered all good.
Unlike modern Portapotties, which seem distressingly vulnerable to attack, The coastal poop pipes were supremely camouflaged against NAZI U-boot attack and later Russian sewer infiltration. Of course, how many public sewers do you see flowing directly into American waterways versus those of the old soviet block? My guess is the Ruskies beat us on that one.....