There is no good reason not to.
I use a freelancing site where this is rampant.
In terms of usage, one of the annoying factors of a Javascript only link: right click is a vital tool for me, and I never use it to access the save to disk on images, which is why many sites disable right click (which doesn't stop anyone anyway.) Right click->open in new tab/window. It may seem trivial, but when you have a lot to do, need to access many pages at once (and don't want to sit around waiting because they take too long to load) and have assembled a few fast ways of doing it, this is like that stop sign with the hand: we won't let you do that, do it our way or don't do it.
One of the biggest reasons is that search engines (and other devices) don't execute JS, and you're missing an opportunity for internal cross linking. Just have a blank page with all the links in your nav, maybe even supplement it with other content.
It's really easy to do, the only reason I can think of people don't is they don't know or are being lazy.
<a href="alternate-content.html" onclick="return some_function(this.href);">link</a>
Then in whatever "some_function" does, end it with return false, even if you don't need to pass the href:
function some_function(url) {
alert('The href is ' + url + '.');
return false; }
Returning false stops the page control from executing it's natural action, in this case, navigating to the href. When JS is disabled or not present, it's ignored, best of both worlds. It's one of those things that is so easy to do there's no reason not to.
