LBB Book 2 has an ECM program you can buy for your ship's computer. Like everything in the LBB's, it's pretty basic: when the program is active, all incoming missiles are destroyed on a roll of 7+.
I've also argued in other forums that the High Guard combat rule that applies a +/- to-hit DM based on the relative difference between the ratings of opposing ship's computers must be a highly abstracted version of ECM activity.
Your point is well-taken. Indeed, EW is perhaps a little
too abstracted in HG2 given the
overwhelming advantage bringing the biggest computer to a HG2 battle yields.
As for regular old B2, in addition to the optional rules in Special Supplement 3: Missiles (which I haven't made much use for, and which describe some targeting and sensor systems which are effectively immune to ECM), building on the idea that Tactics skill (and importing from HG2, Ship Tactics skill) is available as a floating DM to pretty much any one roll during each round of combat, I have also allowed enterprising PCs to hack up a version of Gunner Interact that adds skill-based DMs (typically Navigation, but also perhaps Sensor Ops) to a defender's ECM roll when running the ECM program. This would then invite someone to code a B2 ECCM program to offset the base or modified ECM roll, but no player of mine has suggested trying that yet.
(Many players and refs overlook the fact that B2
encourages coding your own custom software; quickly finding and fixing those pesky flaws is trivial if you open-source things, I would expect.)
However, I also allow a second type of missile, the IR Flare, that does a very good job of pulling incoming salvoes off of a defender, and that tends to be a more-reliable option that trusting your luck to an ECM dice-roll -- so long as the magazine holds out... there's a pleasingly realistic symmetry there: if you rationalize that by default space-combat missiles are IR-homing, as opposed to radar-guided, in order to make them much more resistant to ECM, then they become vulnerable to spoofing via hot decoys.
And thus a sort of balance is maintained.