Typical CRT flicker was pretty subtle, especially at high refresh rates. It becomes more pronounced at low refresh rates, or simply bad monitors.
Making a silly effect on a website to evoke a nostalgic feeling doesn't really have to be accurate, and it'd probably be near-impossible to accurately represent the subtleties of a CRT display without compounding them with the subtleties of LCDs, especially so when the LCDs an end user will be using is an unknown.
Certain parts of the past are not worth emulating :)