Yes, it was done by using different back plates of the cartridge like shown here.
I remember all it took me was using pliers to remove the blocking plastic on the back.
I would guess you instead modified the slot to simply accept both.
was it really a security feature?
Yes, and it worked well.
Did Nintendo really think that was enough to stop people from playing cross-regional games?
Most important here, grey imports are still regular sold cartridges, so royalties go to Nintendo, just Nintendo Japan instead of Nintendo USA. This is a big difference from copying games.
Beside that, the expected damage would be rather minor. It wasn't about making it impossible, just making it inconvenient - and most of that is already done due to the fact that it's not an English language game.
As the saying goes: A lock isn't about keeping thieves out, but honest people honest.
Game companies don't earn most of their money from gamers dedicated enough to:
- Import form overseas
- Circumvent protection (modify cartridges)
- Live with foreign packages
- Live with foreign text manuals and
- Accept foreign language on-screen text
Less than half a million people in the US speak Japanese, that's about .15% of the population, not much to loose. Out of the remaining 99.85% not many would go the length to buy a Japanese version if they can get an English at a similar price (or even lower as prices in Japan were rather high).
That leaves only a very dedicated minority of collectors - a group that no protection measure can really stop. Someone like that would simply buy a Japanese console as well.
It never pays to fighting for 100% control if 90+% can be reached with way less effort.