Theory #1 - Holograms are so last millenium
The technology being used (on Krypton) is over 18,000 years older than the technology in the shuttle. It's quite reasonable to assume that in that time, fads have come and gone. It may simply be that modern Kryptonians are into metal communicators this season.
Theory #2 - Holograms are less energy-efficient
One of the key reasons that council inadvertently destroyed Krypton is because they were mining the core of the planet for energy. Assuming that holograms use up more energy than the metal displays, then it makes good sense to use that option rather than having costly holograms all over the place.
Theory #3 - Holograms need a fixed surface (or a plug socket)
In the film, holograms are only used in fixed installations (e.g. where the projector can be mounted to a wall or flat surface) whereas the metal "pin art" communication system is capable of free-floating within a mobile structure. It may be that the holograms need to be connected to the Kryptonian equivalent of mains electricity to work properly.
Theory #4 - They're re-tasking equipment intended for another purpose.
The 'liquid metal' face of the bots can clearly be used to transmit video but that's not what they're actually intended for. The whole point is that it's the bot's literal face, intended to communicate with the user but presumably in a way that couldn't be mistaken for an actual person.