Yes, Apple silicon Macs will have Thunderbolt ports
https://arstechnica.com/gadgets/2020/07/macs-with-apple-silicon-will-support-thunderbolt-apple-says/
Macs with Apple silicon will still support Thunderbolt, according to Apple. The clarification came after Intel's Thunderbolt 4 announcement led many to speculate that Macs without Intel CPUs would not have Thunderbolt ports.
Here's Apple's statement, which was provided to The Verge: