One of the first things I do when starting a new game in Uplink (and this does take some time), is to download all of the servers from InterNIC and save a route that includes every single one. Of course, I start the route with InterNIC and the Uplink Test Server. After that, whenever a mission calls for a server that's already in my route (99% of the time), I just load the route and then double-click the target server. Usually, I need to zoom the map in a bit to pick out the target since it's cluttered full of names.
The double-click on the target is actually registered as two separate, single clicks. The first adjusts your route so that it includes the rest of the systems in the original route, but removes the target. The second appends the target at the end of your route.
Do the above, and you'll find that most systems will have trace times running upwards of five minutes! That's more than enough time to do whatever you might need to do on most systems.
Something that helps manage the chaos of having so many system connections registered, is limiting the number of systems that are displayed on the map by default. In the connections list on your Gateway's home screen, you'll notice that each system has a little icon to the right of the system's name. By default, this icon should be two circles. This means that, unless the system is part of a mission you have queued, the system will be displayed as a white square on your map. Click this once, and the icon will turn to a plus sign - the system is now an orange square on the map. Click it again, and the icon (and the system on your map) will disappear. Usually, I use this to set my map up so that it only shows essential Uplink systems, InterNIC, and whatever systems I'm currently working on for a mission.
I haven't done any testing to see if having this long of a route is actually overkill but I do imagine that, after a certain number and/or type of servers are added to your route, there probably is a point of diminishing returns. Fortunately, Uplink doesn't emulate the actual network performance impacts that such a long and complex route would have, and you only ever need to remove logs from one system in the route (I usually use InterNIC) to break the passive trace chain, so there's really not much of a down-side to this.