Hi Zoran,
IIS does not serve the .vb files which constitute the UI layer of the DotNetNuke application (which are available here anyway), and proper ACLs prevent unauthorized editing. Since DNN is not (and really cannot be) strongly named, and the base code is publicly available, even if the "publish website" codeless deployment scenario were supported, anyone breaching your server could just replace an assembly and achieve similar damage to server-side code changes. In most setups, you are likely neither more nor less secure with the .vb code on your website.
The main benefit from precompilation relates to application performance. I know that one reason that DNN does not support website publishing relates to its custom handling of localization; it is perhaps possible that in the future that this functionality will be migrated to the ASP.NET 2.0 localization system and the deployment option will be back on the table (if localization is, in fact, the only thing preventing it).
A couple security guides are available under Resources/Documentation/Downloadable Files above, including DNN Installation Hardening, at http://www.dotnetnuke.com/LinkClick.aspx?fileticket=qkVjRRDHNwU%3d&tabid=478&mid=857.
Hope this helps!
Brandon