is it possible to add a config so we can change Navi's flight speed, and/or how much ammo you get when you buy it?

You can modify the values in the weapon's lua file. Just install the mod manually (extract the .gma from /addons (there are guides if you don't know how), put the contents into /garrysmod), then navigate to garrysmod/lua/weapons/navilauncher.lua, open with text editor and you can edit the values.

"SWEP.Primary.DefaultClip" = amount of ammo you spawn with, "SWEP.Primary.ClipSize" = ammo in a clip. For the speed locate "velocity = velocity * 500000" near the bottom and change the 500000 to something else. If you set it too low it might do less damage as the damage is produced by the physics.

If possible, you should randomize the sound played from a pool of Navi's voice lines. "Watch out!" would be especially funny. :P

Done :)
It's going to randomly alternate between these two voice lines now. I find the other ones too short personally, but if desired I can add more.

Nice! Thank you so much! :D

Im more wondering if you could potentially make this an actual gun so that it doesn't vanish from your inventory upon switching weapons