Right now researchers and the Tainan city government is urging the central government to give them funding to excavate the sites. If they do get their funding, perhaps they can lift a ship or build a museum around it.
So far, the best Dutch sites in Tainan would still be Fort Zeelandia (Anping Old Fort), and Fort Provintia.
You would find Fort Provintia unrecognizable. After sacking the place, Koxinga made Fort Provintia his home. Later when his passed, the place was used as a ammunition storage, and later just abandoned. Several temples and schools were built on the ruin, which are the basis for the structures standing now. When the Japanese rediscovered the original gate to the fort, they turned the place into a museum.
You sort of can see the foundation of Zeelandia at Anping. The standing structures have all been replaced also. Although a lot of the damages to the structures were caused by poor maintenance and people taking apart the original structures for building materials, the two Dutch forts weren’t very earthquake proof themselves.
Another place you could see is at Sicao (四草) Dazhong temple (大眾廟). There is a concrete tomb for fallen Dutch VoC soldiers. The remains were moved to its current location in 1971, after being dug up by local construction. Although DNA studies of the site were never released, and there’s no way of knowing if the bones found actually are of European origin.
You may also visit Lu’ermeng (Lo̍k-ní-mn̂g 鹿耳門). It first showed up in Dutch records as Lacquymoy. It was the place where Koxiga slipped through Dtuch defensed and into the lagoon to directly lay siege to Provintia.
There’s also the National Museum of Taiwan History in Tainan, where you probably can find some expert on the issue.