hi wcp86, i've checked with my ID and he said HDB stipulates at least one ventilation vent must be kept clear. My ID sealed the 1 directly on my dining area and left the other one (where you described) unhindered so its okay i guess.
it depends on the type of trunking you're intending to get. one ID i've found when I visited the spring home deco in expo 2 months back told me that it's possible where they can scrape a small part of the surface of the ceiling to place the trunking in nicely (trunking must be the long and flat kind).