I'm getting a Decker ready to play in a buddies game with the max In Debt, National Fame, Trust Fund, and Day Job.
As long as I don't lose my job or piss off my trustee, then I should be able to make the minimums with my passive income, letting me apply most of my surplus 'running pay to the principle.
Edit: Oh yeah, to actually answer OP's question. I read that you technically get the karma, but it has to be spent on the 5k each.
"IN DEBT
BONUS: 1 TO 15 KARMA
Whether it came betting the ponies or buying that new
pony, the character owes money to an unsavory third
party. The player and gamemaster must work out the
details, but the happy thing is, for every point of Karma
(up to 15) spent to be In Debt, the character gets 5,000
nuyen to spend during character creation. These points
are spent in place of the normal Karma for extra cash
and extend the possible additional funds to 75,000¥."
I get how it could be read the other way though. I chose to read it in the way that didn't benefit my character, since he's already kind of questionably built.(HORAY DEATHARM)