I want to automaticaly add version parameter to all my theme scripts and styles, to get something like this:
<script type="text/javascript" src="/themes/mytheme/Styles/common.min.css?v=12345"></script>
Are there some ways to do it by Orchard CMS?
Have a look at the Combinator module on the Orchard gallery.
It will fingerprint your resources, as well as combining and minifying them if you want (all configured in the admin interface)