Thosse "barnacles" are actually vermetid snail shells, they are a hitchhiker in reef tanks. I don't think they will raise your pH to any noticeable degree but they are very sharp, I've impaled my finger on them quite a few times and I could easily see a large cichlid blinding or injuring himself slamming into one of them. I would snap them all off at least so they aren't sharp. A file might help to do this.
As far as cleaning the tank, it can be a real pain to get coralline algae off things. Your best bet is probably a long soak in the vinegar solution, and then attack it with a strong sharp razor blade or similar metal scraper, while being careful not to scratch up the glass.