Oh it is an issue. But it is debatable if you will feel it if you are running a single slow-medium BC quarry in single player and doesn't have much else going on. But it is not something you want going on large scale on a server or on a already complex world.
Everything you have loaded and running in MC will take time for the server(you have a server aspect in singleplayer too) to process every tick. A Quarry with a lot of fluids in it will take up loads more time to process than an empty one. But if your world is simple enough for everything to be processed inside the normal tick time then you wouldn't feel a difference. Your flooded quarries might take up 90% of your server processing time, but if it manages to process it all in normal time, you experience it as all fine.
But on a multiplayer server (or a sufficient complex world) things are different. If everybody start using bad solutions like this, then your server performance is bound to tank is no time. The server will simply not be able to process all the information in the allotted time and your ticks start lasting longer than they should(TPS) and certain things never get processed(blocks you place vanish again etc.).
There is a reason why Quarry solutions like "Ender Quarry" and "Quarry Plus" were designed specifically to not cause fluid updates. The authors didn't just randomly decide to give them this feature, they were specifically build with this in mind because the BC Quarry have big problems with this.