A few thoughts ....
There are some new air scripts in the Ed Depot, one of them is a kind of Shilka warning receiver which makes a satisfactorily alarming ping ..... you could try installing that - its quite atmospheric.
Instead of just Shilkas, have some of the border patrolled by AA soldiers. If the are moving then the exact place that is covered is constantly changing, so you can never be sure whether they will get you or not. Maybe if put their skill level low they will miss a lot, which could make for some nice missiles trails in the sky.
Make sure you cover the coasts so that the player can't simply just fly out to sea and back in again.
You should always reward skill in the player, so place your Shilkas in the "correct" places: guarding bridges, road junctions, towns etc. The player can then look at the map and think "hmmm, that route is likely to be guarded." Also guard the most obvious by-passes .... but leave the less obvious ones unguarded, you've got to be able to get through somehow.
Place some Shillkas next to woods or buildings ..... then the field of fire is blocked in one direction. Means that you can fly relatively close to one without it being able to shoot you, which might help with the tension level.
Use a trigger with music when the pilot gets close to the border. Very atmostpheric, music. I find the regular Death music quite off-putting when it starts in the middle of a mission.
Use titletext to flash up a big warning on the screen - "Beware AAA!" - as you cross the border.
Use doMove to make a friendly AI contolled chopper fly ahead of the player as he gets near the border .... then teleport in (and out) an AA soldier to shoot it down with a missile. Hopefully the player will see it and wet his pants. A kind of cutscene in a way, but as part of the playable game.