I have an Aquatica for my Canon 5D Mark II.
If you are in the actual business of photography it pays to have the best port. I have some small scratches on my acrylic port that I have been using for several years and they don't affect the image at all so yours must be pretty deep. I have used a soft cover that I can quickly release to protect it. It takes an additional second or two but it has spared me the issues you have encountered. In a place like Truk I wouldn't have a problem because most of the shots would have been somewhat staged (i.e. had time to set up the shot) and thus not an issue. A place like Palau where pelagics come and go quickly it can be different story unless you are hanging out at a place like Blue Corner and strapped in due to currents with the big fish coming and going. I only get two to three weeks of diving a year so I can't compare what your time under water is but like I said I haven't had the small scratches affect the photos.
The acrylic dome tends to cause the dome side to float up and was putting some stress on my wrists until I added weight in a funky kind of arrangement set up by the folks at Cathy Church's dive center. It's a pain but it works. With glass you don't need as much weight if at all but then the glass requires somewhat more float support. The one thing when diving I have done is to have the camera in my right hand with neutral buoyancy and pull the unit behind me to somewhat protect it also (while in more open spaces). The strobe are tucked in tight and easy to flare out when I do this to save a little time. It also cuts down on the drag. In tight spaces I have the unit in front of me since I sometimes use the focusing lights to act as a flashlight as I travel through wrecks or caverns. It gives me better control when the unit is neutral in my opinion.
I did have a smaller dome port on my Canon S95 housing and it was made of glass. It scratched to the point it was useless so to use it again would mean buying another.
I have bought a second housing and ports on ebay and wet pixel at great prices. You can a lot of times get steep discounts but you have to set the both sites up to flag you when the dome ports pop up on the radar screen because they will go fast. Be patient if this is your strategy since they are not always on sale.