My concern is, not having built anything like this (I'll be making a
mockup with some with MDF when I get a free moment)- what do I need to
worry about? If I'm cutting into 2" post square stock and putting a 1"
high by 1/2" tenon into the post every 6 inches am I severely
compromising the carrying capacity of the wood?

No. The compressive strength of wood along the grain is very high. The
likely mode of failure would the the assembly bowing out. The wood on the
outside of the bow would be in tension and the wood on the inside would be
in compression. The wood in the middle is not under stress.

have you ever drilled holes in floor joists to run plumbing or wiring? When
you drill ahole in the middle it ahas nearly no effect on the strength of
the joist. If you notch the top or the bottom, you have significantly
compromised the joist. The mortises are in the middle so they have a minimal
impact.


Or is it going to be
"OK" because the tenon (ideally) will fit perfectly and continue to
transmit the load to the floor.

The other 1.5" of material is plenty to carry the load.