Yup. The long high-capacitance snake cable will eat all the highs from your nice high-Z pickups, and you'll get a very bassy, muddy, and dull tone. The higher the impedance of the pickups, the worse it'll be: going through a snake with the raw pickup output is the best way to turn a Telecaster into a noisy Gibson EBO bass with nylon tape wound strings that you'll ever see... (;-)
Note for EBO lovers: that was a joke!
Seriously, though: high-impedance single-ended stuff like guitars and basses need to have the minimum possible run of low-capacitance cable to their preamps. Once the pickup signal hits a gain stage that has some drive capability, _then_ you can run it through the snake with little trouble: but even so, you'll probably never be able to recreate the exact tone you'd get with the amp right there and a minimum-length cable.
Note that that gain stage doesn't necessarily have to be a super high-zoot preamp: if one of your stomp boxes buffers the signal even in bypass, then *it* can be used to reduce the effects of the long run. Best of all is to get a good preamp with a balanced output, though, and then you dodge the entire HF-loss, noise-injection problem. But one size does not fit all: you'll need to try it and see, to find out if any of your pedals can act as a line driver for the long run. Your ears will tell the tale, muy pronto.
