star trek - Could you fit a Borg cube in the Voth city-ship?

No

This picture comparing the two (to scale) should help to answer

These images are from the excellent Jeff Russells Starship Comparison Guide

The figures used to create these images to scale are from Memory Alpha - citing the Cubes size as

...measuring over three kilometers across and possessing an internal volume of 27 cubic kilometers.

VOY: "Dark Frontier"

And Memory Beta - citing the Voth City Ship as 4,900m long

Even though this only confirms length, the to scale drawings show clearly that the Borg Cube would not fit inside the Voth City Ship as it is too tall.

For Deep Space 9 - you might be able to squeeze 1 DS9 into the Voth City Ship if you got the angles right, (and if the Voth City ship is wider than it is tall, which it appears to be). Or many more if you took the pylons off/pushed them down.

Size of DS9 as given in Memory Alpha

Rick Sternbach's drawings for a four-foot miniature (six-foot as built) specify a scale of 70 feet to an inch, resulting in a conceptual diameter of roughly 3,360 feet (1,024 meters).

The visual effects department used 5,280 feet (precisely one mile or 1,609 meters).

For Star Trek: Deep Space Nine Technical Manual, Sternbach compromised at 1,451.82 meters (4,763.19 feet), although the new size matches only Doug Drexler's images of the exterior in the book, not his cutaways which depict a smaller station.