I don't think the hydroids have anything to do with the Aptasia, just coincidence.
The shrimp should roam the tank, when the lights are off, they aren't very active during the day, for fear of predation. Some Peppermints eat the Aptasia, some don't. Give them a little time, they worked for me. I only had a couple, but they were gone in a few days.
I don't think any type of certain flow patterns will keep the hydroids from spreading. Just try to treat small clumps at a time with the Kalc paste.
I have some colonial hydroids. I've tried cutting them out, pulling them out, covering them with rocks to cut off light, just about everything I could think of. The only thing that seemed to work was hitting them with Kalc paste. I do have a Copperband Butterfly that seems to tear off the crowns of them occasionally, but I wouldn't recommend one for this purpose, unless you are commited to taking care of this type of fish. Most only eat pods, unless eating other foods at the LFS, mine was, and they are quite delicate. I've had mine for about a year now, but its in a 180 reef, with only 3 other fish.
IMO/E, your best bet will be the Kalc paste.