Well, regarding a simple 4-way adapter like IDE-fix or EIDE'99, which allows to connect four devices to the existing IDE port:
Will I have trouble with OS3.9?
Make sure you install the latest driver software for the 4-way adapter. OS3.9 itself only sees the first channel, you need the driver software to access the second one.
Is the second IDE channel bootable?
No. You could boot from the first channel, load the driver software resident into memory and then reset, then you can boot from the second channel until RAM is cleared. This works with IDE-fix software at least.
(just in case I decide to install Linux, or something...)
Linux clears all memory, so it does not work with the second channel. And AFAIK it does not have a driver for 4-way adapters.
Does the second IDE channel show up in Early Startup Control?
No.
And regarding alternative controllers like the FastATA1200 (aka Powerflyer) or IDE-Fix Express:
I don't know. It all depends on the firmware of the controller (or if there is a firmware at all).
If the controller only works with installed driver software (like above), then all of the above applies here, too.
Bye,
Thomas