The looming thread of side-channel attacks on SMT systems has been known since well, before we had SMT systems (because it also can apply to Co-Processor, and non SMT multi core systems).

The difference between back then and today is "we believe it's possible but haven't found a way yet" and "there are multiple known ways", as well as it being wide spread known instead of just in some communities.

The reason we still shipped the problematic CPU's is because improvement in perf. and as such competitiveness and revenue on the short term where more important.

There also was a shift in what people expect from security and which attack vectors are relevant. For example user applications a user installed where generally trusted as much as the user. While today we increasingly move to not trusting any applications even if they are installed by a trusted user and produced by a trusted third party. Similar running arbitrary untrusted native code from multiple untrusted users and "upholding" side-channel protection wasn't often an important requirement in the past.