A recent check of the website for citizen services at the US Embassy in Tokyo and consulate in Osaka shows that reservations of deposition rooms are still suspended, with rooms unavailable until further notice. This has been the situation since the pandemic struck here and shows no sign of changing any time soon.
Options for parties wanting to take depositions of personnel normally resident in Japan include having the witness(es) leave Japan to be deposed, in which case attorneys and support personnel such as interpreters and reporters can either be at the location with the witness or participate online.
We provided interpreting services in just such a manner last year after the pandemic struck. Prepping was done online before the witnesses left Japan, after which the witnesses travelled to the US and the attorneys and support personnel were spread over several locations in Japan and the US. It worked quite well and eliminated concerns about having to be tested before leaving Japan (a non-trivial issue) and concerns about the return to Japan being troublesome because of possible quarantining.