In my opinion, "counts as" means that, subject to certain conditions, a certain thing counts as something else. Which is crazy-vague, but let me try to explain
:
Any counts-as statement must have three distinct parts: Condition(s), Recipient(s), and Effect(s). So, to use the example of Frag Assault Launchers, "Models using a transport vehicle with this upgrade count as having frag grenades in the turn they disembark." Here we see the Recipients first - models (nice and general) - followed by the first Condition - using the transport vehicle with Frag Assault Launchers. Next up is our "count as" statement, followed immediately by the Effect - frag grenades. Last up, it states the other Condition, which is the turn that the models disembark. Within the confines of the Condition(s), the Recipient(s) receive all benefits of the Effect(s). So, in the turn that models in the transport with FALs disembark from the transport, they receive all the benefits of Frag Grenade. This means they get the initiative boost when charging into cover, as well as the ability to make a grenade attack against a vehicle.
You could break it down short form like so:
Frag Assault Launchers
Recipient: Models
Conditions: 1) using the transport vehicle with the upgrade 2) the turn that the models disembark.
Effect: "counts as" having Frag Grenades
Or we could look at the recent Skimmers Moving Fast debate the same way:
Skimmers in Assault
Recipient: Skimmer
Condition: Being assaulted by a model with a Weapon Skill
Effect: "counts as" having moved more than 6"
Sometimes a Condition will not be stated, which means that the model is always considered to have the Effect(s). For instance, the Brood Lord:
Unnaturally Strong or whatever the hell
Recipient: Brood Lord
Condition: -
Effect: "counts as" having a Power Weapon
Note that I can't quite remember the wording for this one, but the upshot is that Brood Lords receive all the benefits of having a Power Weapon without fulfilling the usual requirement (i.e. actually having a Power Weapon). So, in close-combat with Necrons, the Brood Lord would negate WBB rolls (assuming there are no Res Orbs or Tomb Spiders nearby), ignore armor saves as usual, etc.
Hopefully that makes sense. As has been noted, there are a lot of "counts as" statements out there, but I reckon you should be able to break them all down like this.
Cheers,
-H