I am just guessing but it is possible that the transmission on the engine is beginning to slip.  How does the transmission oil look?   Also is the transmission running hot when this problem occurs?   The transmission would see increased loading during wind/ waves and might not slip at lower power settings so if it is getting weak this is when the problem would tend to show itself.   If the transmission is slipping a lot it might be possible to see if the output shaft from the transmission is increasing in RPM as it should as the throttle is advanced during a period when you seem to be losing thrust.  Again just totally guessing but I have experienced a slipping transmission on one boat and it behaved a bit like this.

Best of luck,

James

SV Sueno,  Maramu #220