My own interpretation tends more toward -- at least for big weapons like the heavy ion cannon of ISDs or the Hoth ion cannon -- the weapon being a maser equivalent of the turbolaser.
That avoids the problems of self-contained bolts of plasma zipping around. The effect should be the same, since the maser-style weapon would also produce a massive EMP effect, following cracks and crevices in the surface of the target like waveguides, following those waveguides into the interior wherever the opportunity presents itself.
There are, of course, a few possible objections to my interpretation.
One is that the guns are called "ion" cannon, not microwave cannon or maser cannon. However, the ion cannon ionizes the targets systems, so that name matter can be explained away easily enough.
Another objection is that the guns don't destroy their targets outright. A maser naturally would not necessarily outright destroy or even visibly damage a target constructed of durable Star Wars-type structural materials and armor, and protected by Star Wars-type shields. Something less durable, like a Star Trek starship, might well be gutted by such a maser attack. It must also be kept in mind that throwing what must be megaton, gigaton and even teraton-level bolts of highly charged plasma would be similarly destructive, if not even more so.
The final objection I can think of is that maser weapons would be hideous antipersonnel weapons. The obvious answer, again, is that a highly charged plasma bolt would be similarly unhealthy, and would leave the target similarly crispy.
This does, of course, require the visible portion of the bolt to be a comparatively harmless tracer element like that of a blaster, laser or turbolaser.
That then leads to the need to explain the impact of the ion bolts on the ISD in ESB. I would then assume -- disregarding the "ion cannon ignore ray shields" bit from West End Games -- that the ion bolts arrived on target at the same time that the actual EMP beams of the shots managed to batter down the ISD's shields. The Hoth ion cannon was certainly a heavy capital ship grade weapon, and if heavy turbolasers of approximately equivalent power are supposed to be able to batter down capship shields, then the Hoth ion cannon should have been able to do so as well if it used a brute force approach.
The defensive value of an ion cannon for ground fire instead of a turbolaser might then be in terms of the disabling effects of an ion cannon attack. Even a minor breach of the targeted ship's shielding could lead to shipwide temporary outages, allowing the defenders to take appropriate action while the enemy is temporarily out of the fight.
I could very well be way off base with my assumptions, but I'm rather fond of them.
