Some Japanese stores shrink wrapped either the cart or the case. Trader is a good example of a retailer who shrink wraps homecarts.
To my knowledge SNK did not shrink wrap games at all. Carts that arrive in shrink wrap or boxes that do, have been so done by a third party.
All old style case games were sealed by SNK with a large sticker with the Neo•Geo logo (in white) printed on it. This applied to both US/Euro and Jap games.
This sticker was also applied for a short while to Japanese snap-lock games until phased out some time in 1996.
A much smaller black sticker with a colour Neo•Geo logo was used on many 1996 snap lock releases, but by 1997 SNK had ceased bothering to seal snap-locks. The new sticker is so small it's pretty unsuprising they stopped.
Seals on snap locks is pretty sporadic - just like the whole warranty card issue.