They do not redirect around blockaded systems, so keep the routes clear of player/pirate outposts. IIRC, routes only change if subsidiaries are moved. A steady income of rare luxuries may more than make up for the decreased raw dust yields. If you spot a rare luxury, don’t be afraid to drop a sub on that planet in particular. Planets in the way get food/industry, while the yields come from a percentage of dust/science/luxuries of the start and endpoints. Subsidiaries should be placed as far away from the HQ as possible because the trade routes are determined by the shortest distance between the two. HQ should be built on/next to systems with high dust/luxury output.
Keep that in mind when shopping for real estate. Edit: resource collection occurs on the system of choice, plus anything one hyperlane away.