I get a big laggy spike everytime a transport leaves. My ping never changes but I see the drones start to drift. Sometimes it's 6 seconds or longer. I was trying to bot on Saturday with almost humorous results. As you can see everytime a transport left I died.

[Sat Nov 27 12:21:44 2004] 0050f0[202] Transport left for Initros System, Sector D-2
[Sat Nov 27 12:21:44 2004] 0050f0[202] Transport left for Initros System, Sector D-2
[Sat Nov 27 12:21:44 2004] *Orne Guardian JT-9014v destroyed Hoax

[Sat Nov 27 12:59:34 2004] 0050f0[201] Transport left for Divinia System, Sector M-14
[Sat Nov 27 12:59:34 2004] 0050f0[201] Transport left for Divinia System, Sector M-14
[Sat Nov 27 12:59:40 2004] 0050f0[201] Transport left for Divinia System, Sector M-14
[Sat Nov 27 12:59:40 2004] 0050f0[201] Transport left for Divinia System, Sector M-14
[Sat Nov 27 13:00:02 2004] *Orne Guardian TP-0826l destroyed Hoax

[Sat Nov 27 13:31:58 2004] 0050f0[202] Transport left for Initros System, Sector D-2
[Sat Nov 27 13:31:58 2004] 0050f0[202] Transport left for Initros System, Sector D-2
[Sat Nov 27 13:31:59 2004] 0050f0[202] Transport left for Initros System, Sector D-2
[Sat Nov 27 13:31:59 2004] 0050f0[202] Transport left for Initros System, Sector D-2
[Sat Nov 27 13:32:13 2004] *ApuTech-17 Guardian DFC-9455-07 destroyed Hoax

[Sat Nov 27 16:12:32 2004] 0050f0[202] Transport left for Latos System, Sector B-6
[Sat Nov 27 16:12:32 2004] 0050f0[202] Transport left for Latos System, Sector B-6
[Sat Nov 27 16:12:52 2004] *Arklan Guardian XR-2899c destroyed Hoax

I've never had that problem. Maybe you're just not paying attention to where the guardians are :P

But seriously, I've never heard of anyone having lag problems when a transport jumps out.

I was just testing this out, and it actually seems true. A slight "hickup" in behaviour when they launch, and when they warp.