That's why I had my mine/base seperated, but still. More of my tricks:
Simply look for their name in the ground if they haven't seen you.
Press "F" repeatedly from a long distance to make the land start rendering again and you can see people/mobs no matter where they are for a second.
We also had portals, so I could sometimes pay off somebody to give me a portal name/password to warp into their base.
Or, have them build a warp gate in the wall somewhere, light it with pumpkins/glowstone to make it undetectable, warp in through there.
And if I REALLY wanted to kill them (even though I detest doing it), get them to let me in their base myself, help them for a few days, then when the log off one day, do maximum damage to insure they that they rage quit (which is much like the equivalent of death on an anarchy server).
If they never go back to their base, that's still a win, because I have created enough worry that they can't use it, which means that either:
A) I can use it if I know where it is.
B) They can't use it at all, which sets them back time/material-wise, while they're making a new base, which gives me an advantage over them in fights, making new allies/towns, etc.
If I destroy that base, they usually fall back to their old one, which restarts the process. If I want to find somebody, I always can; it just takes a little more time for some than it does for others. Funny story: a lot of people from jkeller were playing on a deathban server (about 10 of them) that was supposedly "really tough", even though it had faction protection and such. In 3 days, they had already destroyed the most powerful faction of 30 people on the server, destroyed all smaller bases, and allowed one faction to live because they were somewhat neutral with them. We know how to do it on the jkeller4000!
To quote that "This is Halloween" song: "That's our job, but we're not mean..."
lol