Indeed, it sort of makes continuity sense that they'd only use this special, isolated system when they really had to (that is, when the regular systems were fried), and afterwards would abandon it as soon as they could.
It would be a bit like finding out that your torpedo boat's radar and navigation computer are down, and bringing aboard a handheld GPS to compensate. The GPS is a cool civilian gadget, but you wouldn't want to have to rely on it for real.
Similarly, you wouldn't want to use the silly holocommunicator for any serious work. It can only show you one person (worse than the main viewer), requires you to divert your attention from the regular viewers and consoles and turn around, and may even confuse you at a crucial moment into believing that there's a real person standing on your bridge...
Perhaps after a few weeks of testing, finding a better place for this curio on the bridge, tweaking with the settings... But the first impressions probably weren't favorable. I mean, the device forced Sisko to confront the hyper-annoying Eddington almost "in person", resulting in stress and humiliation that could have been avoided with the use of a regular comm system.
Timo Saloniemi