Hi Triton1,
I'm going to ask you to suspend belief in your instrumentation for a few minutes.
The first thing I'd like to point out is that your BF150 is NOT developing full rpm at all. It should be propped to turn 5,800 to 6,000 with a normal (your normal) load aboard. Your WOT rpm of 5,300 is way too low for the BF150.
The BF150 has V-TEC, which is variable valve timing. It kicks in at 4,500 rpm and when it does the horsepower curve goes from that point right to the upper right hand corner of the graph. It never falls off like a traditional engine. Rated horsepower (150) occurs at 5,500 rpm but MAX horsepower (160) occurs at 6,000 rpm. In a sense by limiting the rpm to 5,300 rpm you're not even getting the horsepower you paid for; you're certainly not able to take advantage of the V-TEC to reach maximum horsepower.
I am not saying that I think changing props is "the" answer (unless the hub is slipping) to the current issue. I am saying that your boat is "over-propped" and that in and of itself will keep the boat from attaining the performance it should with the BF150 on the transom. In the over-propped condition you don't have a stable base line to work from and it very well might be contributing to what you're experiencing now.
Back the suspension of beliefs (at least those surrounding the instrumentation)...
What you describe isn't possible (this is why I'm asking you not to say "but I saw that" for a moment). It's just physics as applied to boats and propellers and it just comes down to math. The pitch of the prop is the distance the boat will move with one revolution of the prop with no slip of the propeller (and no slip never happens really). We have a mechanical connection between the engine and the propeller via the drive shaft, the pinion gear (in the lower unit) and the prop shaft. Unless one of those things breaks (in which case no power transmission occurs) we always get the same prop shaft rpm for a given engine rpm. That's a given and not subject to interpretation. The prop will also turn the same rpm as the prop shaft as long as the hub in the prop is intact and not slipping.
In order for the boat to achieve 25 kts at 5,300 rpm and later 13.5 kts at 5,300 rpm the prop would have to be slipping a great deal. While that's not impossible it would be highly unusual for it to be repeatable and linear and it wouldn't take long for the hub to completely break free and provide anything more than trolling speed.
It's also not possible to add 600 or 700 pounds to the boat and have it nearly halve the speed and maintain the same rpm and fuel burn. Adding weight increases the load on the engine (meaning it requires more horsepower); for the same speed the rpm will increase, or for the same rpm the speed will drop. And more horsepower always equates to more fuel burned (in the same engine).
It's also way out of the range of "normal" for the CD25/BF150 combo to return the speeds you're talking about even with a great deal of weight aboard. That's not "fact" but given the number of CD25s with Honda BF150s on the transom we know what is typical for that combo and 13.5 kts at 5,300 rpm isn't it.
I'm open for almost anything because strange things can and do happen but I'd say in this case that either something in the drive train has literally broken (and for the life of me I can't think of what that would be) or there's a problem in the instrumentation.
The variables (as I see them at this point, so subject to change) are the tachometer and the prop. You can eliminate the tach by pushing the throttle to the stop and getting your GPS speed (ignoring the tach as you can't over-rev the engine and hurt it). If, with the throttle at the stop (regardless of the rpm), you're getting 13.5 kts then the issue almost certainly has to be with the propeller; either it's slipping in a very strange way or because you're over-propped it's pushed you into a "behind the power curve" situation (the available hp just can't swing the prop).
You can now resume your observations and beliefs!

I'm not questioning what you're seeing at all. That said engines, boats, and props behave in certain ways and a behavior that falls outside that norm is suspect. That's the case here. So I'm coming at this from a technician's logic standpoint looking at the mechanical aspects and setting aside the "strangeness" of it which may make me sound skeptical, which I'm not.
It's hard to know what to recommend. Certainly checking the engine with the Honda HDS software will not hurt but I can't think of anything that would result in the situation you describe. Nothing in the EFI system is going to let the engine turn 5,300 rpm (where it always develops the same amount of horsepower) but let the speed drop by almost half.
Given that BF150 is always putting out the same horsepower at a given rpm and that relatively simple math will tell us how much horsepower is required to drive the boat at a specified speed that doesn't leave much for variables. I still suspect you're getting bad data in some way; this in no way implies that you're not seeing what you're seeing, only that something about the data is very suspect (like the tach is set to the wrong pole setting or has gone wonky, or some setting in the gps has changed, etc). Basically, the engine itself isn't going to up and give you half the speed for the same rpm so whatever is happening is happening somewhere other than in the engine itself. It could (remotely) be the prop (slipping or sizing) but it's more likely a data issue.
See if you can grab a Garmin Nuvi or a Tom Tom or a handheld GPS unit and verify that the speeds you're seeing show up on a independent unit. Also check the WOT speed with no regard to the tach reading. I'd also change to a prop that gives you the correct rpm for the engine with your heavier load (should be 5,800 to 6,000 rpm). That should be about a 14 x 15 prop on the BF150 on the transom of a CD25; there are several choices so the numbers can vary but in my experience the BF150 will not swing a 17" prop on a CD25 (especially not a loaded one).
Sorry for the wall of text. Hope it helps at least somewhat.