I would say Hyperdrives wouldn't work through the wormhole.
The reason being you need to input the coordinates of point A and point B, with calculations of things like gravity wells from planets, known blackholes and other anomalies.. the problem becomes if you say point A is one said Y of the wormhole, and point B is on side X, the hyperdrive will try to calculate a route normally.. it wouldn't take into affect a wormhole, not without a lot of programming.
Just make it flat out this wormhole has these effects..
Takes x rounds to travel through the wormhole at safe speed (2500 ft/rd) with a Pilot check DC 15 using established path laid out by navigation buoys at each end.
1) Speed restriction of 2500 ft/rd (let's say this is one-quarter impulse speed) or suffer 1d20 per 500 ft over 2500 ft/round, points of damage direct to hull, bypasses damage reduction per round of travel through the wormhole. So a ship travelling at 3000 ft would suffer 1d20 damage.
A Pilot check of say DC 15 +1 per 500 ft of speed over 2500 ft can reduce damage by half, but this DC increases each time the ship fails the Pilot check.
2) Due to energy fluctuation, discharges, other particles/graviton waves, etc, energy shields, defense fields, cloaks don't work while in the wormhole. Sensors are at one-quarter range, targeting systems grant half bonus. Can't use FTL drives, hyperdrives (Nav Comps can't calculate due to the wormhole gravity well), warp drives can't form warp field, etc.
3) Tractor beams that don't use gravitons work in the wormhole (some groups can tow ships while some can't due to the type of tractor beam systems they use).
4) Upon exiting either side of wormhole, due to energy flux of the aperture opening/closing, Sensors, targeting systems at half range, energy defense systems (shields, fields, cloaks) are inoperative, engines at half speed for x rounds (say 1d6x5 maybe? that would be a minimum of 30 seconds to 180 seconds or 2 minutes). Also FTL systems are inoperative during this time. Repair & Computer use checks DC xx can reduce the time by half.
5) Piloting through the wormhole without downloading info from nav buoys is DC 18 +1 per 500 ft over 2500 ft of speed, each round of travel.
6) Combat in wormhole is dangerous.. Energy weapons deal 50% more damage to target PLUS 50% damage to the ship firing. Same with explosions. Projectile weapons suffer -2 to attack rolls due to gravitons/whatever causing physical weapons to not fly straight. Each time a ship is damaged by weapons fire (their own or enemy) the Pilot check each round is increased by +1. Failed Pilot checks ship suffers 1d20 points of damage as if they were traveling faster than 2500 ft and failed check.
7) The wormhole is only z feet/miles big (width and height, length is how many rounds x 2500 ft at safe speed), so restrictions in how big a ship can be to enter the wormhole, and how much room there is to move around (so nothing the size of the deathstar).
