One approach is to create dummy haks with the same name as the missing ones (each containing at least one file). The module will then open, allowing you to delete the haks you don't want.
If there are a lot of missing haks (too many to discover one by one) you can open the module with NWNExplorer 1.63 then examine Module Data > module.ifo > Mod_Hak.List.
Taking a step back, if you think the haks are still in the hak folder, perhaps you're opening the module in the wrong folder?
I've read of cases where the NWN installation was confused, some files in c: (which I'd recommend) and others in c:/Program Files or whatever.