For the 6502 there were manuals that detailed how many clock ticks every instruction takes and what happens during the ticks, which is pretty much the same.
It’s not like these instruction were ‘secret instructions’ reserved for use by a secret cabal. They’re just leftovers from ‘don’t care’ parts of the microcode. I remember there’s quite a few that simply hang the processor because their microcode doesn’t include the ‘increase the program counter’ instruction so it turns into an infinite loop.
The PDP-8 didn't really have undocumented instructions. It's just that the OPR instruction was "execute immediate as microcode word". There were a lot of ways you could flip those bits to get different effects, and people gave some of them their own mnemonics in third party assemblers, but the effects of the bit patterns were fully publicly documented by DEC and distributed with the machines.
Same was true with pretty much all non microcomputers through the 80s.
Every 6502 family datasheet that I've read described how many clock cycles an instruction took (since that was critical for some applications), but not what happened during those cycles. That was considered an implementation detail -- and did encompass some externally observable behavior, particularly in terms of what happened on the address/data busses during multi-cycle instructions.
Here's a typical datasheet from Rockwell, for example:
It's also worth noting that the architecture diagram on page 5 of this document isn't entirely accurate, either. It's closer to a programmer's model than an RTL description of the CPU; some "hidden" registers used during certain operations (like indirect addressing modes) aren't shown.
What is the other 99.999% of information? Yes, there was some undefined behavior that was not in the official manuals but certainly not a 100000 times what was in there.
Pretty much every Dec and IBM machine up until the 80s.
Bitsavers has the documentation for the PDP-11/40 I used to have here. http://www.bitsavers.org/pdf/dec/pdp11/1140/. It includes microcode listings both assembled and as flow charts. My PDP-11 had actually been modified before I got it with the microcode ROMs in ZIF sockets, as someone had been writing their own microcode.
(Barely-public documents like patent filings don't count.)