The = is a padding character in Base64 encoding:
See https://en.wikipedia.org/wiki/Base64#Output_padding
WinSCP displays it, but does not require it.

The SHA-256 hash in WinSCP key fingerprint warning hash has an additional "=" character in the end. Bug or a feature?

This is also visible on the documentation, on the screenshot on this page: https://winscp.net/eng/docs/message_host_key

I get the same behaviour when connecting our internal SSH server. This is problematic when trying to instruct users to check that the hash matches the one published in our intranet. OpenSSH show the hash without the equals sign.

Using WinSCP 5.13.7 on Windows 10.