if i'm involved in the production as well as engineering, i'll definitely record the guitarist's effects when tracking. Why? Becasue I'm not a guitarist, and I don't own the guitarist's effects. That means if I try to reproduce what the effected guitar sound was, i will be doing it from memory (which ain't too good these days) and without the same exact effects boxes.
That also takes a lot more time. So for everyone's sake (my client's wallet and my laziness) I find it better to find a sound that works and then just record it. A whole lot less to worry about later.
It's kind of like a telling a sax player: "don't play with any vibrato. if we decide we want it, we'll add it in later with autotune. cause it's easier to add in than take away."
To be really safe, you can always take a dry (pre-effects) signal from the guitar and print it to a seperate track, especially if you have some doubts about the effected sound. But in general, anything that's an integral part of the performance of the instrument (like a Leslie on a B3, or a mute on a trumpet) - PRINT IT and fahgetaboudit!!!!!