Random page spread in Alden. Note that I will only check ships that have been definitively linked to the actual target using japanese records for obvious reasons. Also, I'll round the tonnages.
APR 1944
Claim___________Actual
7200t AK.............3800t AK
3600t AK.............7600t AK
5500t AK.............216t XAM (yes, 216 tons, I didn't drop a zero)
3500t AK.............6900t AK
9300t AK.............2100t AK
7000t AK .............976t AK
4000t AK.............6600t AK
4000t AK.............5400t AK
5000t AK.............4900t AK (woot! finally, something close!)
5700t AK.............2300t XAP
4100t AK.............806t APK
7500t APK...........11,700 XAP
7500t AK.............5200t AK
9800t APK............8800t AK
900t ODD.............870t PF (ODD in ONI lingo, this is spot on)
I'd be willing to bet that the mast height different between a 7000 ton AK and a <1000 ton sea truck is pretty profound.
<EDIT> BTW, that random page seems to put the lie to my saying they universally overestimated, lol. I still think that overall, this is somewhat true, these 2 pages out of 226 not withstanding. Of the above 15 stats, 8 are over-estimates, 2 are accurate, and 5 are underestimates. Of the misestimates the smallest error is 1000 tons, and the largest is 7200t. So if they were not universally overestimated, they were almost universally MISestimated. For the mast height issue there is no difference, since it's the relative difference that results in a mast height estimation error.