I dug out a small shard of glass and then pushed the tyre with my thumb, a slight hissing sound came out. So consistently with the slow leak, it appears that there was a very very small hole in the tube, it might have held up till I got to work but I didn't want to risk it. So instead of removing the whole wheel, I just popped the tube out to patch it where it was. This was the first time I'd ever done a repair this way after reading about it many times.
Five minutes later and I have a patched tube ready to go. This was a much much faster way to fix a flat on a hub geared chaincase bike than removing the whole wheel. The only caveat is that you have to know where the puncture is on the tube, not particularly possible on a noisy roadside where you have no chance to hear a hissing sound. I'm a little unimpressed with the tyres however, I would have though such burly tyres would be nearly immune to glass shards like the Vittoria Randonneurs I had on the 3-speed which barely showed any nicks or cuts after the same amount of mileage (approx 3000km). I've updated the My thoughts on tyres post to reflect this. From this experience, I've made sure to regularly check for any embedded glass in these tyres - not something I feel should be necessary for a day to day commuter, not a race bike. Thanks for reading.