Edit: sorry, looking at the RMSS version. Disregard if you are looking at the RM2/RMC version.
There are a bunch of instant spells that last 1 round, stacking is irrelevant for those since you can only cast 1 spell per round so you'll never have more than one anyway. Aside from those, we have Weapon Enchantment (permanent), Loyal Weapon (permanent), Weapon Expertise (reduces fumble), Cleaving Weapon (works as a tool), Protect Weapon (cannot be broken), and Nemesis Weapon (level 50 mastery spell).
I don't see any issue with allowing all of those to stack. Weapon Enchantment is a prereq for everything else, so that has to stack. Loyal Weapon is also permanent, so not stacking would be problematic. Cleaving Weapon isn't really a combat spell, so no concerns there. Protect Weapon is a fairly lame spell if it forbids the instant spells from being used. And Nemesis Weapon is 50th level, at that point doing crazy things should be part of the bargain.
The different versions of Weapon Expertise of course would not stack with each other.