In reader 3.1.0 when red lettering is turned on (NASS/KJVS) the Strongs hyperlinks are overridden.  Having Strongs hyperlinked words is a very cool feature but if red lettering overrides it then it's not quite as useful in my opinion.  I don't know if this is working as intended or a bug.

Nope, you're absolutely right -- it's a bug.  To fix this, we've gone to underlined words instead of blue words in the next release.  (It's a lot easier to read, I think, with underlined words, whether they be red or black words, they're less distracting than the blue links in 3.1.0.)