It does not mean OMG or awesome. It's a stand-alone phrase, usually preceding the phrase that will describe the object or situation that's freaking you out, blowing you away or leaving you at a loss for words.
It's present tense, denoting something that's actually happening and feels like it is beyond incredible.
Holy mother of pearl! That's some serious shit.
Holy mother of pearl! That's one strong fuckin drink.
Holy mother of pearl! Did you see that?(a flying dog playing a guitar and shooting laserbeams from its eyes)
A spaceship appearing over London would leave you speechless, probably only with the ability to utter the words 'holy mother of pearl.'