Heating pads I have found can be quite shite.
Is it me, or is that pic of the newly forming roots on that clone...-those nodules seem to be forming above the water layer? If that is so, it would suggest that the roots would form much quicker in an aero-clonning situation..ie even more air....mist as opposed to water with bubbles.
I think, regards the holes I would just tend to have larger holes and remove the clones as soon as they have some root growth...ie pot them up early. Once they have some roots they are away.
The aero clonners I assume consists of simply a summerged water pump in a resevoir bin filled water(heated)...and then on the end of the hose is placed a suitable nossel to create a 'mist' which fogs up the 'clonneing container'. If that is the case, I could see one major disadvantage of such as system, and that would be if the water pump failed, potencially the clones could dry out quickly....unless of course, in the clonning bin, any excess water returns to the resevoir, except for an inch or two which remains in case of pump failure...an inch or two of water would maintain humidity such that mositure levels would be ok for a number of hours or days if the pump failed...blah blah
Alternativly, where a pump failure happened due to mechanical fault...two pumps would be used.
If I did go with aero-clonning, instead of dipping clones in hormone, I would simply as you suggest, use a liquid based rooting hormone diluted in the water.
There is nothing worse than taking a number of clones and only getting 25%...that sucks. Aero here we come.