I had this issue for several days. On last Saturday I rearranged my layout so that the impact is minimized.
- Stockpiles, chests and workstations can be the bottleneck if there are too many storage in an linked area. I solve this by separating them into groups. Items can only be moved between groups when I put a cart at certain position. Each group has 3-10 stockpiles/chests/workstations.
- Smog particles seem cause lag as well. We start large production orders by using multiple smelters just before everybody go offline. We login only after the massive smelting is done.