No it would not? Pre-patch/expansion fights would be the same as always while later ones would incorporate weakpoints. We already have "targeted limbs" (boss in Sunken Temp, WoD Hydra, boss in Toto-Rak) on some monsters without breaking the game or having every mob redesigned, how would it be any different with just having a flag on new monsters vs old ones?
Also, I wouldn't be surprised if some of that original underlying code is still there. We still have elemental and weapon type specific damage (blunt, slashing, etc), they are just "disabled" currently. Check the combat logs, and it will say "monster hit with <element> damage".
Well, seeing as SE doesn't seem to be afraid of changing base rules (ie: no base class for exp classes), I don't see this being a problem if they were to go ahead with something like this. Also, if a player was going to fight a certain monster with a certain weakness, would they not build their strategy/rotation around that fight? Wow, going in with the same rotation you use on every monster may not work and you may have to change things to cater specific monsters. Everything is fluff, you can break the game down to "make the number go higher". It makes the game less monotonous and goes beyond the memorized "do job's rotation" and "do the certain mob's dance".