It varies a lot, but last time I was there (which was for the 06:50 flight within the last 2 weeks) I was in the lounge within 20mins of arriving at the airport at about 5am. But on the other hand if I had needed to stand in the CX Economy check-in line it would have taken a LOT longer. And on a previous occasion I waited 45mins for immigration alone. Remember that MNL has a separate internet check-in counter, so if you have checked in online (and can quote your boarding number) you can bypass the Y-line even without status.
The Philippines is currently one of the "no liquids/gels" places, but I decided to chance it, and my toiletries were not detected. They are hand-searching some, but by no means all, bags. Shoes may now be kept on "unless the machine beeps", but belts with metal buckles need to be put thorugh the x-ray!