I have no experience with the Zero or SAMD in general. If you look at the source of the Arduino SAMD Boards' Wire library
you can see it's written to support up to 6 channels:
#if WIRE_INTERFACES_COUNT > 0
extern TwoWire Wire;
#endif
#if WIRE_INTERFACES_COUNT > 1
extern TwoWire Wire1;
#endif
#if WIRE_INTERFACES_COUNT > 2
extern TwoWire Wire2;
#endif
#if WIRE_INTERFACES_COUNT > 3
extern TwoWire Wire3;
#endif
#if WIRE_INTERFACES_COUNT > 4
extern TwoWire Wire4;
#endif
#if WIRE_INTERFACES_COUNT > 5
extern TwoWire Wire5;
#endif
so you would just be able to use the standard Wire library functions prepended by Wire1, Wire2, Wire3 instead of Wire just as documented in the reference.
However, if you look at the variant file for the Zero
only one is enabled:
#define WIRE_INTERFACES_COUNT 1
The only variant with more than one (2) is the Circuit Playground board.
Is the reason that those pins aren't broken out on the boards?
So the quick hack would be to simply change the value of WIRE_INTERFACES_COUNT in variant.h and see if it works. The real way to do it would be to create your own hardware core that references the Arduino SAMD Boards package for as many components as possible but contains its own board definition and variant. There are already a couple of these sort of hardware packages in existence that could be used as a model, and in fact it could be worth checking if any of them are configured for more I2C channels.