NESmaker by default sets the mapper's mirroring type to vertical mirroring. The mirroring type is a part of the hardware, even if your game doesn't take advantage of it. For Mapper#30 it can support both vertical and horizontal mirroring, but can't change its mirroring type during gameplay. So yes, you should use the right mirroring type for your game.
I personally have used horizontal mirroring for my recent NESmaker projects, which you can change in your game's iNES header. But if you haven't messed around with that, vertical mirroring is the default your game will use.