Hi,
to answer your first question:
<script type="text/javascript" src="/mbl.nsf/xsp/.ibmmodres/.js/Test1.js&Test2.js"></script>
/.ibmmodres/ is internally used by the domino server. It is an identifier how to handle the current request (with a module, not as an on disc-resource).
<script type="text/javascript" src="/mbl.nsf/xsp/.ibmmodres/.js/Test1.js&Test2.js"></script>
The /.js/ behind this is the identifier how to handle the following ressources (as a javascript ressource).
<script type="text/javascript" src="/mbl.nsf/xsp/.ibmmodres/.js/Test1.js&Test2.js"></script>
The names of the script libraries for internal identification (this is a "tribute" to the mime handling which uses the file name of the requested resource for type identification).
The idea behind is to minimize the requests to the domino server for a better performance of web pages.
To answer the second and third question:
No, it is not a bug. The name you give to the resources is your free choice. You can name them whatever you want to (with/without extensions) etc. This is the name inside the "$Title" Field, and is the Notes name. In the package explorer you see the files "raw", that means that eclipse stores javascript files with .js extension.
Hope this helps
Sven