Good point. I didn't have Assassin's Cloak until fairly late in the game and actually didn't even bother with sniping most of my playthrough unless I was in trouble. My cooldown was mostly used for Heavy Reave, not Cloak. Between fearing infinite respawn points and the amount of health enemies have on Insanity, I saved my sniper rifle for Krogans, Scions, and large Mechs. The limitation of the Mantis's 10 shot capacity, scarcity of clips, and often being pinned down were enough reasons for me to ditch the Mantis after Freedom's Progress.
EDIT: Also, mathematically, the Mantis is still less damage. Even if you cloak up every shot for 75% and cloak up none of the shots with the Viper, it's 4,604 total damage to the Viper's 4,914. It also sucks less when you miss and has less wasted damage to overkill. Your preference is your preference, but there is no real advantage to using the Mantis over the Viper compared to a number of disadvantages.