According to this source, there were an estimated 3.6 million EU nationals in the UK in 2016, of whom 2.4 million were in work. The BBC Suggests 2.9m and 2.15m. That gives between 0.75 and 1.5m not working - assuming roughly half of these are under 18, we end up with between 2.5 and 3.15 million people over 18.
ONS figures give a total population of 65.6m, of whom 81% are over 16*, so roughly 53m people of voting age.
Therefore it's roughly 5-6% of the population, depending which figures you believe...
Caveat: I don't know if those figures include people who have dual nationality, or Irish, Cypriot or Maltese citizenship, so it will probably be lower than that.
*As pointed out below, voting age is 18, but those ONS statistics don't break down 16-18 year olds.
were excluded from the 2016 EU referendum
andspecifically because they did not have [B/I/C/M] nationality
seem to imply that they had some right to vote at that referendum to begin with, but no UK or EU law grants such a right. You could as well be asking why Kim Jong Un was excluded from voting in the 2016 POTUS elections. Maybe you should change the wording of your question?