Should I blow air canister over MacBook motherboard?
I use a commercial can of compressed air (versus air from your shop compressor, for example) and gently blow any and all dust from the exposed interior. I would do this before proceeding to replace the drive, especially if there is visible dust in the interior.

I pay particular attention to any cooling fans (not knowing your exact model) to blow all of the dust off the fan blades and from the ductwork. A pair of tweezers or a toothpick can be helpful to remove major dust bunnies, if any.

Try not to blow dust up into the fan spindle/seat directly, nor into your hard drive or Superdrive (which is simply saying, be careful to blow dust OUT of things, not into them). There may be an exposed pressure port on your hard drive case (non SSD), and the mechanism and optics in the optical drive, which are not friendly to dust or too much air pressure.