First, let me say I'm no RAW fanatic, so I often discuss making a few mutually agreed house rules to adjust for RAI on some issues in friendly games. This would be one of them. Since we're told to only discuss RAW in this forum, that I am doing.
That said, my RAW take on the "Ignores Cover" special rule in the rulebook is that it applies only to weapons with that rule that are shooting at models that can take wounds (i.e. not vehicles). For example. if I shoot at a skimmer in cover with my Thunderfire Cannon using the airburst type of detonation, then the Raider DOES get a cover save against glances and penetrating hits. That is because the TFC has the "Ignores Cover" special rule (and the "against wounds" modifier in the codex). This would apply to any other weapon that has the "Ignores Cover" special rule, or has a description in it's codex that says "... against wounds".
To my knowledge (I don't have every codex), the only weapon that currently explicitly has the "Ignores Cover" special rule in it's codex is the Thunderfire Cannon. All the other ones have separate descriptions which indicate under what circumstance the weapon ignores cover saves. Some include the words "... against wounds" (e.g. Inferno cannon), and some have no such limiting qualifier (e.g. Deathstrike Missile, Hellfury Missiles, Eradicator Nova Cannon).
The old rulebook had the "against wounds" modifier in the description of template weapons, then new rulebook gives template weapons the "ignores cover" special rule which also has this limiting modifier so effectively there is no change for template weapons.
So in summary, if a weapon has the "Ignores Cover" special rule, or is a generic template weapon, or has the "against wounds" limiting modifier in it's codex entry, then vehicles hit by them are entitled to cover saves (if applicable) such as conferred by the Jink special rule or being sufficiently obscured from the firing model. If the weapon does not have the "Ignores Cover" special rule and does not have the "against wounds" limiting modifier in it's codex entry, then vehicles hit by them do not get a cover save (from Jinx or otherwise).
Again, I don't play it that way (unless forced to), but that is what the RAW is as I understand it. Hopefully GW will fix this with an FAQ before they nerf more weapons by giving them the "Ignores Cover" rule in their new codexes.