In my sci-fi rules, ECMs fall into roughly 3 categories.
First, there are countermeasures that I consider passive from a rules perspective. These would be things like the reactive armor that you mentioned or could be infantry CQ deterrents on vehicles. For these, I work the advantage into the base stats/abilities for the unit in question and give a description for the statistical bonus when compared to units without. Note, these can be offensive or defensive in nature. However, they are always in effect.
Next would be defensive counter measures that require activation. These are items like IR flares that grant a defensive bonus when activated but for a limited time.
Finally, there are offensive counter measures that require activation. These are items that can jam or hack systems, but that require you to actively target units. These can either debuff a units offensive capability [ie to search or target], or they can buff the units [or a friendly units] stats [ie stealth]. These are similar in final effect, but they differ in mechanic and metagame interaction.
All of this is done very simply due to the level of abstraction I use, but I feel it is an effective means of modeling the role of counter measures in general.
http://bombshell-games.com/