I don't generally believe in using master engineers for targeting cannons (which I do not recommend in any case) or mortars (which are ok but you can find better).
I also do not believe they should be equipped with the hochland rifle, repeater handgun, repeater pistol or grenade launching blunderbuss (all of these are available in one way or another to your Handgunner, Pistolier and Outrider unit leaders)
"Why ?" you ask.
Because it will distract them from using their pigeon bombs !
Flying pigeons with bombs strapped to their underbelly are not only essential entertainment but they are actually very useful indeed. I normally use them to pick out enemy artillery early on, or find a weedy unit with low leadership to try to rout (especially gobbo units suspected of harbouring terrorist ball and chain fanatics !) . If the enemy is foolish enough to have any exposed heroes, lords mages etc with no accomplaying unit then they can also be targetted.
From experience I have found them more reliable and effective than the much larger area effect mortar. Once again though it depends on who the enemy is. It's no good firing them at anyone with a reasonable armour save but one or two pigoen bombs can easily rout a unit of goblins shielding some fanatics.
Try them out, I usually take at least one into battle - you won't look back.
PS. they really, really annoy the enemy who can become obsessed with sending your engineer to heaven as your brave pigeons unravel all your opponents best laid plans :)