The article you cited is obsolete. It was originally written in 2008, and apparently when updated in 2015, some of the outdated information was left in place.
The version refers to the particular algorithm for signing the request. These AWS services have deprecated the older, less-secure methods (signature versions 0 and 1) and will no longer allow them after September 2009.
Indeed, versions 0 and 1 are not supported.
A few AWS services don't support signature version 2:
Amazon Simple Storage Service: You can still use HTTP with Amazon S3 and securely make authenticated requests. The service uses a different secure signing protocol.
This is also inaccurate. S3 supports signature version 2 in all regions where signature version 2 was deployed. Regions launched in 2014 or later do not support V2 at all, they require Signature Version 4, and in those regions, S3 also requires Signature Version 4.
Importantly, though, none of this has anything at all to do with HTTPS.
From the same document:
Most AWS services accept HTTPS requests, including:
...
Amazon Simple Storage Service
Okay, so, let's revisit this line:
The service uses a different secure signing protocol.
This statement is not about encryption, or security of the payload. This is a statement about the secuity of the request authentication and authorization process -- its resistance to forgery and reverse-engineering -- whether or not the request is sent encrypted.
HTTPS is supported by S3, to protect data in transit.