Microsoft SmartScreen - suspended using Inno Setup installer?

Nowadays, you have to use EV code signing certificates.
See Transferring Microsoft SmartScreen reputation to renewed certificate.

Below is the original answer, which addresses some specifics of the question.

If you believe the problem is due to an unsigned uninstaller, make sure you set the SignTool directive of your Inno Setup project accordingly. And make sure SignedUninstaller directive has its default value yes.

Quoting SignTool directive documentation:

Specifies the name and parameters of the Sign Tool to be used to digitally sign Setup (and Uninstall if SignedUninstaller is set to yes). When Setup has a valid digital signature, users will not see an "unidentified program" warning when launching it.

If you want to set NXCOMPAT and DYNAMICBASE flags to the uninstaller, you can create a sign.bat batch file that both calls signtool.exe and editbin.exe:

@echo offeditbin.exe /NXCOMPAT /DYNAMICBASE %1signtool.exe sign ... %1

The calls need to be in this order, otherwise the editbin.exe breaks the signature.

Then use the sign.bat instead of signtool.exe in the SignTool directive.

Though I do not really think this is necessary, nor helps anything.

I think this is normal behavior.When your software collect enough "likes" = downloads or installs the SmrtScreen will automatically turn off this message.

It is really annoying feature because with every software release you need to wait appropriate time while the software become "popular" and it is recognized as safe (no certificates or antivirus methods can solve it).

You do NOT need this "Windows Application Certification Kit".

What @slappy says is correct:

After renewal of your certificate, you need enough downloads and "good reviews" before this message goes away.

What you need to do is to download your application using Microsoft Edge (not Chrome or Firefox!!!).

It will most likely say "This download may be dangerous and has been blocked".

Then you can choose "Keep anyways". And then you can choose "Report as Secure".

And THEN even Smart Screen says that it doesn't trust your app (even though it's digitally signed, LOL!!!!), then you have to choose "More..." and "Install anyways".

Install it on your computer! I think that is important.

I have used 5 different computers and reported my apps as secure multiple times and installed it.

I have also asked 2 friends (because of their different IP address) to do the same.

I hate this so much!!!!!!!!!!After 1 day, the error message was gone.