In the yard you can definitely hear the train passing by, but inside houses with double pane windows it should be pretty faint, not enough to wake you up except the very sensitive type.
Caltrain is electrifying their tracks. Once complete they can switch to lighter electric trains which should reduce noise, at least that’s what they claim. But even the current Caltrain trains are not that noisy, unless they blow the horns. But then if high-speed rails come through there will be many more trains than what we have now so noise level will go up.
I have a rental very close to BART tracks in Oakland. Now THAT IS loud. Even with double pane windows it’s hard to hear anyone on the phone when trains pass by. And BART have many more trains than Caltrain. And BART trains are already electric. My tenants seem ok though.