Though not as good as Dwarf Thunderers, these guys are one of my favourite Empire units. But why are they always a little disappointing in the game?
Deployment with misile weapons is pretty crucial and the challenge here is to maximise shooting while not letting your combat troops get in the way - deploying to one side helps here. Causing panic tests and stripping ranks off incoming enemy units is the goal here. Combat is going to happen eventually - the Handgunners job is to get it more in the Empire's favour. Bear in mind though that with only a couple of rounds of shooting there isn't much chance to achieve that.
One challenge is whether to deploy forward to get the enemy in range sooner or back to slow them down in reaching you. Another is that if you send your combat troops forward too early, the enemy can gang up on them and once in combat are immune to your shooting.
What to do... what to do?
My current stance is to deploy them forward alongside the combat troops. Focus fire on knocking ranks off incoming units and forcing panic tests. Keep firing on one unit until the panic test point is reached then move on to another. You're unlikely to wipe them out but doing this will weaken their combat resolution even if they pass the panic test.
One thing I am a great fan of is the Hochland Long Rifle. This allows your champion to shoot at individual models rather than joining in the unit's shooting. Shooting at enemy combat characters is often disappointing here but good results can certainly be gained when targetting wizards - particularly undead characters whose death means the army crumbles.