So after digging and researching turns out this was fallout from the Apple lawsuit.
Apparently clicking a link opening an app is an invention of apple????? (my ass it was)
Anyhoos, to turn this bullshit off go here and follow the instructions:
http://forum.xda-developers.com/showthread.php?t=1696536
You'll need to be rooted.
Some ROMs already have the offending HTCLinkifyDispatcher and ro.da1.enable set to false in the build.prop. I am using good old Sense so I got wacked by the lawsuit bullshittery.
This had been in effect since apparently June, meaning it hit me with some update 2nd half of the year. I clearly haven't been paying attention.
But now, maps work like they should: I click a link on link in a webpage and voila my amazing and world's best map app, Google Maps, opens.
(This also applies to Play Store links, Maps addresses, and possibly Contact data and phone numbers.)
SUCK MY LONG HAIRY DICK, APPLE!!!