The in-universe explanation might very well be that Shredder died before the 16-bit TF games take place (he's completely absent in the Sega version). Thus, the Cyber-Shredders seen in TF and TMNT3 (Game Boy) were all clones.
The fan-game fighter TMNTxJL went with that theory that his big tumble at the end of Turtles in Time/Hyperstone Heist was a fatal finale:
https://www.youtube.com/watch?v=KaoTqsiO1uU
And because I assist with that project, it's canon in my mind!
