Depends. If the CF adaptor joins that pin to another ground then it should not make a difference (with CF storage) anyway but...
... you might find it causes an issue with "real" IDE devices, which might expect a certain amount of ground resistance and no more. They work OK but they will get hotter than they should, and so will the IDE circuitry (Gayle?) on the A1200.
So prolly OK in short term, depends if that pin is connected to gnd anyway on the Amiga side or the adaptor side.
I would get it fixed though, as it might be the gnd pin for the main power (+5V) used by expansions. OK, power requirements are a lot lower now than when the A1200 was released, but gnd will find it's way regardless - if you are overusing the signal gnd paths because there isn't a power gnd path, that might cause an issue long term (months or years of use).
I say "might" because it also partly depends on the drain of your CF adaptor and how strained your power supply is already.
Your chances of getting away with it are very good, I'd say. But not perfect.
