[jeffnc]

OK, you can ignore marq, and let's get back to the question.

As chandler said, water tends to soak into grout, thereby getting behind the caulk. Organic materials from your body and bath products provides food for mold, and it can grow there. Follow his advice for getting out the grout and letting it dry thoroughly (days, not hours, with a fan).

You have a Schluter system so you don't need to worry about waterproofing or water getting through a grout crack. The concerns about grout cracking in corners (i.e. changes of plane) are are little bit "sky is falling" IMO. And in any case most movement in the framing since you built your shower is over. If it were me, I'd simply grout everything and leave the caulk out now.

If you're not able to clean/bleach the grout to remove the dark color, then you'll need to dig some out. But you're right that you don't want to bottom out and cut through the waterproof membrane. They make a grout saw, but with small mosaics like yours, they're often too big to fit in the joints well. It should be easy to use this tool without bottoming out because it's not real powerful and you can go slow.

QEP Handheld Grout Saw with Contoured Handle and 2 Blades to Strip, Remove, and Clean Grout 10057 - The Home Depot

Complete your tile installing work perfectly and professionally with the assistance of this amazing QEP Handheld Grout Saw with for Cleaning Stripping and Removing Grout.

www.homedepot.com

If that's too big, then you can use a Dremel with a diamond blade. You have to be a little more careful with this one. Also these are expensive and tend not to last too long.

Dremel 7/8 in. Rotary Tool Diamond Wheel for Marble, Concrete, Brick, Porcelain, Ceramics and Epoxies 545 - The Home Depot

Get the Dremel Diamond Wheel 545, for rotary tools is designed to cut through hard materials such as marble, concrete, brick, porcelain, ceramics and epoxies from The Home Depot

www.homedepot.com

Ideally you want to get all the grout out so the replacement grout is strongest, but in your case I wouldn't try take out more than half (depth-wise).

Once the new grout is in, you can seal it which will reduce water absorption, which will reduce any mold growth.