Yes you are missing the point. Applications aren't a problem.
No, your point is irrelevant, you just haven't realized it yet.
To create a shortcut to a folder you have to create a "launcher" and enter the "name" and "command" (not to mention the available icons don't include a regular file folder or disk icon).
No, actually all you have to do is right-click the desired folder, file, app, and click "Make Link"
Icons are located in general folders such as /usr/share/pixmaps; /usr/share/icons, installed icon packs are stored in /home/[name]/.icons.
As a side note I had to also download icons to get a "file folder" picture for my shortcuts. It would be nice if the default list of icons for the "launcher" included the common items stored on a computer (e.g. file folder, disk drive, music files, video files, web, open office, etc).
Most are. Right-click on MintMenu, edit menu, select the properties of any app, click on the icon and it will open the directory it is in.
Linux is both similar and dissimilar to Windows. Not everything is going to be exactly the same, that's the point. Research and learning is the key, do not automatically assume its a system fault when you cannot complete a task
Get out there and figure it out