Prepare for in-depth:
Node checkpoints are a vital strategic, tactical, and economic necessity for the GTVA. Nodes are hubs of traffic, and chokepoints to any incursion.
On the strategic scale, nodes are what determine where the lines on the map are drawn. They are the single most vital form of transportation for fleets on both the attack and defensive. Take the node, cut the lines of reinforcement and redeployment.
Tactically, they are massive liabilities. Any defending force has to keep a tight watch on them in times of war, or be jumped and summarily destroyed by a transiting larger enemy fleet. They also anchor any picket in place, making them VERY easy targets for fighter and bomber wings. Bait them, stay just out of engagement range, distract them while heavier elements move up, or pull them out of position and cut their retreat. Even with subspace, it's still possible to do that within limited volumes.
Economically, they are trade, full stop. The only way goods travel from one system to another, and also the only way communications and people transit as well. Cut it, and you stem the lifeblood of trade, cut the spread of news, and, once again, plug the redeployment lines.
Truth be told, I'm hugely surprised any given (important) node isn't staffed with at least an installation, a few dozen sentry guns (and Mjolnirs) and at LEAST a pair of Cruisers, if not a permanent Corvette with fighter escort. They're just too damned important to leave undefended.
Plus, I bet pirates would absolutely LOVE to jump merchants and freighters that have just emerged from an intersystem jump. Makes a nodal escort and defense even more of an obvious solution.
You guys need to stop thinking of these things like borders that span hundreds of miles like on Earth and instead like thin, difficult to defend, enormously valuable bridges that link together tiny, insignificant islands in the vast cosmos. They are vital and must be defended. Full stop.