Yes they do, every time. Your naked eye just can't pick out small boats doing it. Here is what you do. Get your telescope and focus it on a boat that is moving away. Watch it the entire time through the telescope. If it is a clear calm day you will see it disappear from the bottom up. Every time. I live near a very large lake and have watched several story high cargo ships disappear over the horizon in just this way.

Have a nice day.