Why pass parameters to CSS and JavaScript link files like src="../cnt.js?ver=4.0"?

It is usually done to prevent caching.

Let's say you deploy version 2 of your new application and you want to cause the clients to refresh their CSS, you could add this extra parameter to indicate that it should re-request it from the server. Of course there are other approaches as well, but this is pretty simple.

As the others have said, it's probably an attempt to control caching, although I think it's best to do so by changing the actual resource name (foo.v2.js, not foo.js?v=2) rather than a version in the query string. (That doesn't mean you have to rename files, there are better ways of mapping that URL to the underlying file.) This article, though four years old and therefore ancient in the web world, is still a quite useful discussion. In it, the author claims that you don't want to use query strings for versions because:

...According the letter of the HTTP caching specification, user agents should never cache URLs with query strings. While Internet Explorer and Firefox ignore this, Opera and Safari don’t...

That statement may not be quite correct, because what the spec actually says is

...since some applications have traditionally used GETs and HEADs with query URLs (those containing a "?" in the rel_path part) to perform operations with significant side effects, caches MUST NOT treat responses to such URIs as fresh unless the server provides an explicit expiration time...

(That emphasis at the end is mine.) So using a version in the query string may be fine as long as you're also including explicit caching headers. Provided browsers implement the above correctly. And proxies do. You see why I think you're better off with versions in the actual resource locator, rather than query parameters (which [again] doesn't mean you have to constantly rename files; see the article linked above for more). You know browsers, proxies, etc. along the way are going to fetch the updated resource if you change its name, which means you can give the previous "name" a never-ending cache time to maximize the benefit of intermediate caches.

Regarding:

I am sure that Js/CSS files can't get the parameters.

Just because the result coming back is a JavaScript or CSS resource, it doesn't mean that it's a literal file on the server's file system. The server could well be doing processing based on the query string parameters and generating a customized JavaScript or CSS response. There's no reason I can't configure my server to route all .js files to (say) a PHP handler that looks at the query string and returns something customized to match the fields given. Thus, foo.js?v=2 may well be different from foo.js?v=1 if I've set up my server to do so.

That's to avoid the browser from caching the file. The appending version name has no effect on the JavaScript file, but to the browser's caching engine it looks like a unique file now.

For example, if you had scripts.js and the browser visits the page, they download and cache (store) that file to make the next page visit faster. However, if you make a change the browser may not recognize it until the cache has expired. However, scripts.js?v2 now makes the browser force a re-fetch because the "name's changed" (even though it hasn't, just the contents have).