I have some issues with the passive trace missions that I think Onlink could remedy.

First of all, the username and password they give you for the compromised server doesn't give you access to the logs. You have to use the admin account for that. This is a problem.

Second, you'd think that some people might be willing to cooperate with an investigation if their server was bounced through. Maybe you could email them somehow and only hack them if they don't cooperate? Or to undelete the log?

Speaking of the log recovery, it seems likely that more agents have Log Deleter 4 if Uplink sells it. Perhaps you could go into the console and run a system restore?

Perhaps they phone up each company and ask them the next IP

Well, that certainly would be... real.
Maybe you only get called in if it bounces through a government server, which refuses to give up its logs.