1.) Are they safe particularly the flower group in Pasig since they're the place who have the most reasonable price and very accessible to my office? Hopefully, my neigbor's construction works will be done after this week.

they are relatively safe. stay away from those cheap motels.

2.) I prefer dark rooms, do they (or do most motels have dark rooms?) have black-out curtains (the curtains that you usually find in hotels to make the room really dark if you want to)?

most of the motel rooms in manila are dark enough & conducive for sleep.

3.) Are their airconditioning units really that good?

yep.

4.) Can you hear noise (e.g. traffic outside, and lovers making out from the other rooms) inside your room?

from my experience, no.
it's a bonus though if you hear the moans from the adjacent room. (joke!)

5.) Do most of them have hot shower?

definitely yes.