People did discover it early on as it's inherent in the design of the chips, it just seemed unlikely at the time. Now Intel has to deal with a huge potential liability if something bad happens because of it. It was just bad business.

Also, appealing to common practice doesn't make logical sense.

Here: https://en.wikipedia.org/wiki/Appeal_to_tradition

For competitive markets to remain competitive, actors must receive the right disincentives. Intel reaped decades of competitive advantage by forgoing security for performance. As you said, they decided that the cost of mitigating these known vulnerabilities wasn't worth the benefit. Now it has come to light, and without due punishment, that math will skew even further toward exploitation over safety in the future.

These technologies were created at a time when it seemed to be very difficult/near impossible to exploit them for the purposes were seeing today. Of course Intel should have changed course when processor speed and newer technologies were introduced. Rather, they decided not to worry about this.