If you don't change your carbon filter regularly the chlorine that gets to the membrane will ruin it - I have that problem myself. I used up a DI cart (good for 6800 gallons) making about 60 gallons of water.
I am adding a second carbon filter to my RO/DI and replacing my membrane with a 75...
Well, I never put it in the tank, just as hardware on the hood. It corrodes some, but not to the point of stuff flaking off, especially if you use good quality hardware. I have never had any problems, and I have been using it for 4 years.
YMMV tho...:)
I used your second solution for mounting the fans - Use a 4" hole saw to make a hole in the canopy, then drill 4 holes and use long brass bolts, washers and nuts to hole them on inside the canopy. It looks great from the outside, no problem! It's even better is you have a grill you can install...