I have Encore CS3 1.0 which came with a Library full of templates items like buttons and menus and such.

However in the new, CS3 version i dont see anything in the Library pannel anymore. There is also no Library folder in the program file location as was in previous versions.

There should be some included menus and buttons. I assume you are saying you had Adobe Encore 1.0 and upgraded to Encore CS3. Either way, Encore CS3 does have included templates, I do not know why yours are missing unless you did a custom install and forgot to include them.

The Library can be excluded during install. It is installed if you keep the default presets, but I always skip it at 4-point-something gigs. I wish they included a 100MB selection of simple blank buttons and thumbnail menus regardless, but they haven't since at least 1.5.