Pump impellers are plastic but the drive shafts, bushes and seals behind them are not. Think as well about the time that you spend soaking the cell to clean it. It's relatively quick if you use a strong acid solution, but you're still talking a few minutes. You need sufficient concentration and sufficient contact time for the scale to dissolve.
Then think about the flow rate through the pump and the residence time in the cell. You would be pouring acid in for quite a while to get the cell clean and all that acid is now in your pool. So now you need to adjust your pH, your TA and possibly resurface your pool due to pitting of the plaster.
Seriously don't go there.
PS: Muriatic acid is as corrosive as heck, probably not the best thing for cleaning the cell, although it is fast. Personally I prefer to use a less corrosive option and soak it longer.