I've run without the baffle in my 4-1 a few times, and once I had the entire cone off for non-fun reasons. I never noticed a significant change in performance or anything, but my jetting is a little rich as-is.
A helpful person might respond to your thread with the standard rigamarole of "do plug chops at varying throttle openings to determine jetting" but some people don't like loud exhausts...anyway, I would personally not really worry about it beyond going up a size or two in the main jet and maybe a half turn out on the idle mixture. It'll be fine.
They do have baffles and they are installed, so no need to be mad. There's even a little stuffing inside too. Still they are open enough to make it run lean, even compared to stock. And besides, it's less loud than 90% of Harleys (99?) even if I pull out all the interior of the exhausts so please calm down
As always, the answer depends on the specifics. You may only need to shim the needles a bit or you may need to go up a size or two on the mains. Dynojet may still sell a Stage 1 kit that worked well for many aftermarket systems. There are several ways to check the jetting. The most precise would be to hook up a wide band sniffer to the pipe that can record engine data and go ride the thing under real world conditions.
A less tech and expense intensive method that will get you close is this——