o "start" - If this value is changed after the wiki has been up for a while, for example, changed from "start" to "index," will this break existing links?
If the links read somenamespace:start, then yes, if they read to somenamespace: not.
o "refshow" - what is this setting? References for what, and where are they shown?
This setting is related to "refcheck" which checks if mediafiles are still referenced by pages before deleting them, it defines the number of references that should be shown if there are some.
o "passcrypt" - how is the salt determined?
//prepare a salt
if(empty($salt)) $salt = md5(uniqid(rand(), true));
o "disableactions" - is there a list of actions anywhere?
I recommend to use the "Settings Manager" admin plugin, there you`ll see a list of all actions with checkboxes.
o Media settings - the page says "DokuWiki tries to detect... libGD automatically." Is there a way to determine whether it detected it or not? (aside from uploading an image and trying to view it resized...)
You can enable the "debug" option and check its output. The information about the used libGD should be present there I think.