I'm not sure that the meager information currently provided in clan window is accurately telling us how the workshops (and caravans, for that matter) are performing. I had some wood workshops (left over from a couple patches ago when wood was OP lol), and decided to change some over to something that made sense for those cities & supporting villages' raw products. Two became oil, another went wine, while one stayed wood. The numbers in the clan report seemed to show they weren't doing very much (either before or after the switch), but my daily income rose pretty dramatically. Before, 4 shops + 2 caravans had barely covered party wages. Suddenly started clearing 2000-4000 per day.
In the absence of detailed info (there's nothing at all on caravan profit/loss), I can't conclusively state where the big increase came from, but the workshop switch was the only recent change I had made. And it didn't happen to coincide with the daily patch either.
Not a huge issue demanding immediate attention, but as time goes on and Bannerlord gets more fully fleshed out, I hope they implement some more reports like Warband's. Not just on budget like this, but morale, lord/faction relations, etc.
(EDIT: disregard above. Finally stumbled across the mouse-over tooltip that itemizes shops/caravan profits/wages better than the clan window. Yeah, most of my surplus is coming from caravans. I guess their increased profitability and my workshop switch was somehow just coincidental.)