I've had waves/ripples visible just after boot on my Mac512, but that was fixed when I replaced the caps on the motherboard. But I've never experienced ripples on an SE/30. If you measure the 5v and 12v lines off the external floppy connector and get close to 5.0v or 12.0v when booted, then the source of your trouble is mostly likely the flyback. I'm sure those ancient caps on the analog board could use replacing, but in my experience they are typically not the source of trouble (as bad caps are on the logic board).
I'm not an expert on flybacks though, so I cannot say what will occur if yours blows. The very fact it is cracked makes me wonder what cracked it in the first place. If one contends it was "age alone" then I would expect to see such cracks as a widespread problem, but your report is the first I've heard.
If you're worried (and don't care to conduct a scientific experiment to see what happens when a flyback does blow), then you either have to replace the flyback or your entire analog board.