I bought a 2011 Prius with a bad headgasket. I have repaired 6 of these cars now that have had bad headgaskets. After I got the car running I noticed what I would consider a lifter noise. I drove it about 30 miles and the noise never went away. Has anyone ever had a bad hydraulic lifter in a 3rd gen Prius before. note: I will be checking for exhaust leaks within the next couple days, but I am nearly certain I do not have any exhaust leaks.
Depending on how long it was driven with a leaking head gasket, you might be hearing a rod bearing knock from a damaged bearing due to water in the oil. If that's what it is, it might run like that for a long time.........or it might "grenade" tomorrow and leave parts all over the road.
Presumably the lash adjusters can go bad; there's a procedure in the repair manual for testing them. Have you used a stethoscope or something to better localize the noise? I have daydreamed about bringing a stethoscope audio signal and the camshaft position sensor signal together into a scope or DAW to see if the noise coincides with a cam position, but I've never buckled down and done it.
G3 uses hydraulic lash adjusters. It's a tiny bit misleading to call them 'lifters' in the Gen 3 engine, just because of where Toyota put them. They are the fulcrums under the rocker arms; clever Toyota, as they don't have to move with the rockers, so their added mass doesn't really matter.