Should I mill myself if I have graveyard synergies in my deck, but haven't drawn them yet?
Let's assume the game will end within 13 turns. In those 13 turns, you will draw 13 cards, and since you have no information where the Survivors' Bonds are, the milling has no effect on how fast you draw one or how likely you are to draw one. If you don't mill at all, you will draw the top 13 cards; if you mill every turn, you'll draw the cards at positions divisible by three. (Well, if you're unlucky enough to mill all of them, you can stop milling of course.)

Milling does however increase the value of a Survivors' Bond; without creatures, it's a dead card, and the more options you have, the better.

So bottom line: always activate Skull Prophet.