I can't say its good for them but I will say my turtles also used to do it. keyword: used to...
My new set up I feed them in a seperate tank so after I feel their full and (most always poop right away), I'll move them back to their regular tank a few inches away. Sometimes they'll still poop in their regular tank but now I notice they don't touch it. I'll take it out if I see it since it really messes up water.. especially if they eat it. It seriously clouds up water immediatley and I'm sure adds to the salmonella factor since it came from their insides. So keeping a tank clean alone is probably the main reason you should take out poo if you see it. Just get a net and rinse the heck out of it when your done.
It might also be a sign that their hungry. But if you feed them, I recommend cleaning their poo (or do what I do and do a half water change while taking out any bad stuff)