something thats been bothering me for quite some time now.
Every once in a while, i'm flying through an empty WH sector, make the jump alone and to my surprise, npc's jump exit the WH together with me.

It ruins continuity a bit for me.

So what? It's just the cloaking device in action. It has to recharge, just like the battery, after each WH use.

nah they just dashed across the entire sector while you were loading the next one

Actually, it's because the sector you're going into was not running until you warped in. Sectors containing no players for more than 5 minutes shut down. That way, we don't eventually end up running 7680 sectors (before any future expansion). The bots that are 'traversing' non-running sectors are set to warp into the next sector after a reasonable duration to emulate passing through it. When a sector starts up (as when you warp into it), any bots that were pretending to traverse it, now warp in for real as though they had just gotten there. Ideally, we could estimate where in the sector the bot would be based on where they're coming from and going to, and how long they've been pretending to traverse it, and then place the bots appropriately when the sector starts. But it's not a trivial thing to do right, and we don't feel it has nearly as much impact on fun as other things that take less development time to fix/add.

how do you define reasonable time?
I've seen up to 5 convoys clog up in a sector that was not active.
And when there are not a lot of players online I see hardly any convoys in grey space. (which makes liberations a bit weird because you have to activate the routes of the traders yourself).

Are you sure that stuff is working correctly? Maybe the timeouts are a bit long?

related to this. I think I've mentioned this before but NPC convoys don't seem to start from inactive station sectors either.

The whole convoy thing is completely rewritten along with the new escort mission. Initially, the cause of npc-only convoys starting will still be kludgy (until the new economy is in place), but their ability to reliably start in non-running sectors and get to their destinations, is *greatly* improved. The amount of time they spend pretending to traverse a non-running sector is currently 1.2 minutes. I plan to gather stats on traversal durations in running sectors and ultimately determine the emulated-traversal-duration based on them per sector & direction. At any rate, let's see how the new convoys do; I'll be keeping a close eye on them for a while after release, and I'll make sure they don't suffer from the problems you brought up.

About a week ago I was hunting a constilation I tracked it from latos n15 to dau I-7 (I think) by the time it reached dau I-7 I had reduced it to a flameing wreck bits flying off and all. To avoid tangeling with the sf and the connie I decided to wait till it left the station and then kill it. I followed it to 3000m and watched the conni jump the the arta/dau wh but when I got there it was gone. Why does this happen? Where does it go?

Try docking and riding along to get more insight on the answer to this. :-)

"look... no hands", it despawned.

When an NPC has finished it's cargo run, it jumps to "nowhere".