How clear is the clear resin these bases are cast in?

While it is not perfectly clear like a window you can see through it

This base was hit with a very thin wash of light blue mixed with Future floor polish.  The clear wash helps the clarity because it smooths out the rough surface texture that causes light to difuse and make it look slightly frosted.

Does superglue cause the resin to go cloudy?

Not at all.  As you can see with an extreme closeup of a base with excess glue.  As you can see there is no discoloration or any affect on the resin itself.

Does drilling the bases to pin a mini in place leave an obvious mark on the base?

Other than the hole itself there is nothing obvious in the base to show the pin.
Since I always use paperclips to pin my minis I'm using one for this example:

And the underside of the base with the paperclip pin inserted.  You can see where the pin is if you look closely but it's not really easy to see.

Just an example of what you can do with these bases here is a base that was 'painted' with a thin blue wash and some white plaster for snow.