How can I hide the files while installing my application using an Inno Setup made package? It can be hidden by
"[files] attribs : hidden"
but it again can be seen by activating the windows option
"Show hidden file"
How can I hide it permanently to avoid user tempering with EXE file?
Can't be done. If you nee a detailed explanation why, see this blog post: http://blogs.msdn.com/oldnewthing/archive/2005/04/19/409620.aspx
If you are really ambitious and you really have an issue with people "tampering" with your exe files you can perhaps encrypt your exe files, play with the PE (portable executable) and loader, or other stuff.
I doubt any of that is worth it. EXEs have been distributed by many software companies over the years. Your application is probably not that special to warrant anything out of the ordinary.
Set those flags, and concentrate on more important issues.