Smatty - Can be an issue with an aluminum boat (especially if you have electric start). If you just have an outboard and that's it, you should be fine. 2 things to do though incase. 1, replace the zinc anode on your motor (underneath the bottom fin typically - only a few dollars) 2. Use a rubber snubber on your downrigger instead of your clip - they are about a foot long, usually green non-conductive material (like clothes line) and come rigged at your favorite fish store. That is supposed to isolate any hot charges coming off your downrigger. Also helps to use a vinyl coated ball or one of those new enviro-balls.
To test, you just get a voltmeter that reads from 0-1 V, lower your rigger a few cranks and troll normal speed (away from other boats), then put the positive on the downrigger wire, and the negative grounded to the boat edge - look for a reading from 0.5 to 0.7 - if you are outside of that, you may have a problem.
Black box are considered by many a money pit depending on what you have. The only case they would save you is if you have a big aluminum, electric start, gps/sounders all sorts of electronic crud, and a rusted away anode on your engine! All they do is dial in whatever voltage reading you want as you can dial in a certain voltage to actually attract certain species (ie. sockeye like hot around 0.8). They usually run in th $200-$400 range.
Check the pro-troll website for a thorough description and do a search on this message board or many others for it - tons of discussions on it.
Trolling deep apparently has very little effect though so you should be fine either way - just need to find a place with more fish - anywhere south of Campbell River has been awful this year on the east side, so it probably isn't just you!