You can set up one ship with all the weapons and hullmods you want and then save it as a custom variant. Then go through all ships of the same type and select the desired variant; the ships will now be appropriately equipped.
If you want to double-check each ship to see if they're all equipped correctly, just scroll through each ship and glance at the Ordnance Points bar. If the bar is full, the ship is good to go; if the OP bar isn't full, there's a weapon missing somewhere.
Also, a 100+ ship fleet is very impressive and beyond the "normal" scope of the game -- I think the biggest fleet I've managed to maintain had around 30 ships