This is an interesting observation, tsunami.

The ICOMOS evaluation suggests that it is included:
" The complete reconstruction of the state hall at Shuri-jô derives from scale drawings and photographs of the hall before it was destroyed
by fire, cross-checked with extensive archaeological excavation. The result is an exact replica of the earlier structure, which is of great symbolic value in Okinawa. "

I don't know what the truth is. But I just edited my post.

a. The English Wiki site repeats "In 2000, along with other gusuku and related sites, it was designated as a UNESCO World Heritage Site. However, only the castle relics such as stone walls and old piles before 1950 are officially designated as the World Heritage." But that could of course simply have been copied from the Japanese entry already cited by Tsunami. Unfortunately no source reference is quoted
b. The Nomination File is remarkably opaque about the issue of "Authenticity" despite having a long section on the subject. Nowhere does it clearly state that the reconstructed buildings ARE part of the Nomination – but neither does it say that they are not!! Unfortunately Appendix "4a. Inventory of the monuments and sites included in the nominated property" is not present!! This would appear to be an important paragraph - "In this way the authenticity of the setting has been preserved on a high level while promotion of the property through full-scale replicas of architectural structures or rebuilt structures is pursued with a high degree of accuracy and precision in relation to the authenticity of the setting." I.e what has been preserved is the Authenticity of "Setting" whilst the authenticity of "Design and Material" and authenticity of "Workmanship" in relation to original stonework etc are dealt with separately on the basis of original remains
c. In Dec 2017 ICOMOS ran a symposium which included the presentation of a paper titled "ICOA853: SIGNIFICANCE OF RECONSTRUCTED BUILT-HERITAGE AFTER WARTIME DESTRUCTION: RESTITUTION OF IDENTITY?" which is concentrated on the issues surrounding the reconstruction of Shuri-jo. I have extracted the following quotes
i. "In March 1972, the 'Shuri Castle Remains' was designated as a 'Historic Site' within the Japanese national inventory system under the current Law for the Protection of Cultural Properties (in force from 1950). According to the Agency of Cultural Affairs of Japan, what is protected for the category of 'Historic Site' is basically the land surface, which may also include archaeology." (My bold to emphasise the limited aspects which are fully legally protected)
ii. "Under the reconstructed state hall, archaeology of underground remains, such as foundations, are strictly protected" (my bold - seems to imply that the hall, constructed above, is NOT so protected??)
iii. "Shuri Castle REMAINS was inscribed on the World Heritage List in December 2000 as part of a serial nomination composed of 9 sites and monuments, named the Gusuku Sites and Related Properties of the Kingdom of Ryukyu" (my Capitals and bold to emphasise the potential importance of this word. i.e ONLY the "remains" and not the new reconstructions??)!

See - http://openarchive.icomos.org/2003/1/30._ICOA_853_Okahashi_SM.pdf

None of this unambiguously answers the question as to whether the reconstructed Hall etc were inscribed as part of the WHS or not. There does however seem to be evidence that the original "remains" were and are protected to a higher degree than the reconstructed elements situated on top of them and that the restored/replica aspects are indeed NOT a part of the inscribed site.

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If my memories serve me right, apart from the stone wall which I don't think the fire can do any significant harm, there was a room in Shuri Castle with glass floor that show the little fragment of original wooden remains of real castle underneath it. Such fire may probably destroy those little remains.

Interesting! The Nomination file does mention original wooden remains and includes them under the subject of "Authenticity of Material"
"not only above-ground stone remains but also underground remains are preserved in good condition, guaranteeing the high historical / archaeological value of the property, as a result of implementation of preservation methods suitable for fragile materials, i.e. soil and wood."

Even if the reconstructed buildings were not a true part of the inscription I am sure that the fire has been bad for the archaeological remains as well - stones will have cracked/crumbled and wooden aspects as shown under the glass which would otherwise have been preserved underground will, as you say, have been destroyed

Seems to be just outside the historical village: https://www.japantimes.co.jp/news/2019/11/04/national/huts-burn-near-world-heritage-thatched-farmhouses-shirakawa-go/#.XcBFLehKg2w

Yes definitely outside the inscribed and historic area and therefore not "Connectable" ("Thankfully, the fire began not in one of the large farmhouses in the center of Shirakawa-go, but in a shed near the visitor parking area, just on the other side of a stream from the primary concentration of gasshozukuri structures" - Sora News).
Given the criticism which will inevitably follow the Shuri-go fire it was interesting to note the extent of the fire precautions which are in place for the historic areas of Shirakawa. Indeed it appears that the automatic fire protection system was switched on - "The fire also triggered Shirakawa-go's extremely cool sprinkler system, in which external sprinklers, which are ordinarily cleverly disguised to blend in with the rustic aesthetics, emerged from their hiding places to spray massive jets of water onto the roofs to lessen the risk that sparks or embers drifting through the air would ignite the thatch." (Sora News)
There is a video of the system working in the link provided by Durian - but here is another of a "Fire Drill" practice - https://www.youtube.com/watch?v=6HEkxeK_P5E