Hi!
Thonny has experimental support for WebREPL, which allows editing and running scripts over WiFi (select "<webrepl>" from the port field in the configuration page of ESP32 or 8266), but currently it is not very reliable. I hope to improve this in the upcoming version 3.3.
I'm pretty sure Thonny will never include special support for updating multiple boards (it is an IDE for beginners, after all). I suggest you ask about other solutions in MicroPython forum.
Best regards,
Aivar