For the little window, you can get rid of it with the argument '/q:a'. Exemple:
lpt2prt.exe /q:a

For the security: Yes, this is not a secure way to distribute scripts...
But do you care if one of your 3'000 users think of using WinZip to uncompress the .exe and read the script? Unless it contains passwords...
For me, the use of IExpress is obvious when:
- you need one single file that contains everythings
- that file can be executed on every PCs
- that file is even smaller than kix32.exe
- etc...

Well, isn't it just nicer to have one .exe than many files with 'unknown' extensions?