I approve of this idea.
However, I propose a simplification to this system:
If you own the warpgate outpost on both sides of the warpgate, the gate is shielded and only your empire may pass through it unless the enemy hacks it to temporarily disable the shield. If you lose control of the warpgate outpost on one side, the gate becomes neutral and anyone may pass through it. I just want to stick away from the idea that the outposts will only be hackable if you've lost all other facilities on continents - I am unsure if any single empire will truly ever own a whole continent for long, and though it makes defense slightly harder, it's still just easy to protect your empire's flanks.
Furthermore, this idea of a shield that is only operable when both outposts are protected is easier to integrate into the lore - the shields would be human-built, and not part of the actual warpgate. They would be addons that humans built when they start splitting up into empires to try and have a sense of factional territory.
Also, I support the idea that warpgates serve as links between hexes.