Personally, I think the junker is one of the most underrated ships in the game. It has the fastest turn speed in the game, high armor, and the most guns of any ship of its size. Some downsides are a lackluster speed, hull and (here's the big one) a large balloon that screams 'pop me'.
Have the gunner stay on the bottom of the ship and the engineers split up the bow and stern on the top deck. Use the fact that a junker can turn fast to maximize the use of its guns. It is a firepower centered highly maneuverable platform.
Some builds I like:
Front gun: Flamethrower
Left guns: 2x Banshee
Right guns: Gatling mortar
This build can pretty much handle anything. Crews seem to like it too because it allows them to get on a bunch of different kind of guns. The banshees are for long range, the Gat mortar is for short range and the flamethrower is a defensive weapon to disable ships. It can also be used offensively to charge a ship, burn it, and finish it off with the right guns. Takes a little bit to train a crew to do it right but when you do you're pretty deadly.
Front gun: Artemis
Left guns: 2x Artemis
Right guns: Gatling Mortar
If you point this ship in the front left direction at a target, you will be able to use 3 Artemis launchers at once. Since you have 3 crew members the firepower of this ship is arguably as much as a Mobula at range. Yes it can bring down Mobulas at range. Great for 3v3. This build is also not a slouch at all in close quarters when you use the guns on the right. If an enemy gets close, phoenix claw the ship around to face the right weapons and tell your crew to finish them off.
Front gun: Gatling gun
Left guns: Gatling Mortar
Right guns: Gatling Mortar
This build is totally trolltastic. At the right angles, the front and the right-or-left Gatling gun can be fired at the same time for some fast removal of armor. Then you turn to the mortar to finish a ship off. It kills really quickly, but it's a short range only build and has no fire disable.
There are really a lot of options for the junker and it is easily one of my favorite ships. And yes, it is very viable. Just watch out for hellhound blender-fish.