Imagine space invader in RE engine.
Joke aside. Have experience working in corporate world you will be surprised how many project were actually pushed by lower/mid tier employee than the management. And if those people gone, your favourite game is actually kind of gone too. Unless it's the AAA property , it's hardly being recognised by higher management. In this case it's even worse because it seems to me that Square Enix acquire Taito for their arcade business/operation than the actual product. At the time of PS2 nobody actually care about Taito game anymore. Ex Taito developers might already get merged/moved into the parent company and nobody really have time/power to push Taito side games.
To be fair, missing mid-tier games is not exclusive to just Square Enix, but also every other major Japanese companies.