Best place to put an expander/gate is immediately after the guitar. Much of the noise that comes from amps or amp sims is the original guitar hum/buzz that's now amplified and the potentially negative consequences of using a gate/expander are much less if the noise floor is as low as possible rather than trying to gate out a much higher noise floor post effects.
Keeping the amp gain low can help a great deal with noise, even if effects between guitar and amp are a bit noisy. Which is one reason why many guitarists prefer a clean or "edge of breakup" amp then use pedals to get fuzz/distortion/compression.
The Boss NS2 noise suppressor pedal is an expander which takes things further by having a loop that you put noise-generating pedals in and the loop is only open when there's enough signal at the pedal input from the guitar to open the gate. Set up properly it can block noise quite effectively, though dynamics and sustain might suffer a bit, especially if the noise floor is high enough to compete with the guitar signal as sustained notes fade out. Then the choice becomes live with the noise vs. reduce the available sustain but also reduce the noise vs. rethink gain staging and try and find a less noisy order to put pedals/fx in.
If using an amp sim, I'd track without a gate/expander then insert one as the first processor in the track if it's needed afterwards. That way any potential latency increase is irrelevant.
Noise is not good unless it's an artistic decision to have it. It can really make a mess of a mix because it restricts what you can do if you don't want a mix that's full of noise. There's a reason why good amp, effects and mixer/preamp designers put a lot of effort into designing circuits that have as little self-induced noise as possible.
Pete Cornish's website offers some useful thoughts on why a high noise floor is unacceptable, especially if it's going to be amplified by a big PA.