I actually started with screentones, and let me tell you, they create more headaches than they solve in today's printing. They're real finicky and have to be at a certain resolution to not create moire (the weird checkerboard patterns that pop up with screentones when they print wrong). Even digitally, resizing them for web makes the tones look funky half the time.
I got 80 pages into my comic before saying screw it and replacing everything with flat grays and normal gradients. I still use some texture-type tones that aren't dot based (or I went in and blurred the ones that were), but by and large, using flats has made printing so much easier for me.
I was worried about replacing them at first because I liked the texture it put on the paper and I thought it made it feel more like a "real manga", but I found that the texture look honestly comes more from the paper itself than the screentone. It looks just fine without it, if not better.