Is there an option that the command / nomin can only be used 2 times in one hour , or just how anyone wants to set up ?

There is currently no cooldown for nomini.

Will it come out in a new version?
I ask this because the following situation happened to me. VIP players can use the plugin on the server. Another player stole a minicopter from a VIP player and VIP play is just used /nomini and after that /mymini
That way he returned his minicopter and I wouldn't want that.

I don't think i'll add a cooldown but instead a maximum distance option.

You mean if someone stole a minicopter from VIP player and moved away for example 50 meters with minicopter, VIP player if he uses the command /nomini will not be able to despawn the minicopter ?
of course if my SpawnMini.json  is set up like this:

"MaxSpawnDistance": 10.0,

maxspawn distance is how far away the player can spawn a minicopter from them

And it can't be set to be the same for / nomini in the next version? (maxdespwn)