Thanks for your considered response Adam. It is indeed quite possible that the jump is the non-English pages suddenly being indexed/reported as indexed in this WMT account. If there was to be a 'switch over' of the pages from one sub domain to the root domain, we would indeed have expected to see a jump like that.
It does still seem odd that (1) it came a long time after the migration and (2) the impressions and clicks (as reported in WMT) have not seen a similar jump, neither when the migration took place or in the last week. The 50% increase in clicks from unbranded organic I mentioned was a genuine increase, as our Analytics previously covered all three language sub-domains anyway.
On a side note, regarding the seperate subdomains, I was quite surprised to see how well the hreflang tags worked across sub domains before the migration. It was arguably better handled by Google before the migration to a single domain (more/better sitelinks for branded searches anyway). I think a lot of our uplift in clicks came from new pages and better on site optimization, and that the effect of consolidating the domains was not actually that big (in terms of clicks from unbranded organic). I think that the subdomain/directory debate is not quite as cut and dried as people think.
I must say, I love the hreflang tags - they are one of the most underrated tools in SEO in my opinion. Just don't forget that canonical tag or they don't work!
Thanks again for your reply!