I've not seen vintage stores that specialise in pearls, but there are a couple of stores in Market Market that have a few pieces of pearl jewelry on display. I don't remember the names, but they are in the back of the pearl section and hard to miss.
For all sorts of pre-loved gold jewelry, I frequent "Just Jewels" at the Glorietta 4 Mall in Makati. Occasionally, there are South Sea pearl rings, pendants, and earrings, but the settings can be on the ostentatious side.
But if you're open to new pieces by young designers, check out Bijoux on the second floor of Greenbelt 5. Their new collection features a lot of baroque pearls set in gold and gold vermeil. Plus they're on sale! I myself am going back to have some pearl cage/clasps made for a lariat.
Happy hunting!