This should be "True" instead of "TRUE"

Let's say "RBTools commands may print helpful hints"

"be provided" suggests to me that one could specify a value. Perhaps say "Hints can also be disabled by passing ..."?

Setting the repository type and name each enable different optimizations, and for best results users should have both in their config file. We should probably have separate hints.
Also, FYI, when we're wrapping a conditional like this we prefer using parentheses instead of the continuation character:

if (self.options.repository_name is None and
    self.options.repository_type is None):

This was already mixed up, but can we alphabetize this by key while we're editing it? That'll make it easier to read.

Space at the end of the string after the .

These log messages don't make it entirely clear why the user should set these or what the consequences are of not doing so. How about something like:
RBTools is auto-detecting the repository type, which can be slow. Adding REPOSITORY_TYPE to your .reviewboardrc will speed up rbt commands. Set ENABLE_HINTS=False to suppress this message.
RBTools is attempting to discover the matching repository in the Review Board server. Adding REPOSITORY_NAME to your .reviewboardrc will speed up rbt commands. Set ENABLE_HINTS=False to suppress this message.

Looking at those, I'm reconsidering my suggesting to combine them into a single message, but maybe there's a good way to word a single message without it being too excessively long.

This looks pretty good, but I have a thought. We have these hints right now, but we may want more in the future, and we probably don't want each hint to decide what the output looks like (e.g., the info on suppressing hints being tacked onto every string).
How about defining a new show_hint method on the Command class that takes in a string, checks if hints are enabled, and conditionally outputs it.
That would clean up the code using it now, and make it very easy to start adding new hints down the road.

Looks like .reviewboardrc is part of your change, but it shouldn't be. Can you revert that part of your change?

This is wrapping way prematurely. The docs should have room to breathe. The lines get to go up to 79 characters.

Blank line between statements and blocks, or between two separate blocks.

Thanks, Anahita! Just a few comments below.

Typo in the description: "RBTools current" -> "RBTools currently".
Also in the description, "when it already has not been specified." is kind of awkward. Maybe this can just be "when it has not been specified".

Christian's comment still applies - this .reviewboardrc file shouldn't be in here. See https://github.com/k88hudson/git-flight-rules#i-want-to-remove-a-file-from-the-previous-commit on how to clean that up.

Typo: -no-hints -> --no-hints.

Typo: "will speed up will speed up" -> "will speed up"