At least numerically, the unions have a point. When was the last time that, nationally, a government secured 40% support from the electorate? Even locally, there are plenty of MPs who don't command such support -- 111 MPs elected in 2010 had polled fewer than 40% of the total votes, and if you extended that to include considering votes not cast then the figure would be much higher still.
So imposing this standard on Unions (who are hardly meant to be a shining beacon of democratic legitimacy) and ignoring it in the place where democracy is supposed to really matter strikes me as a massive double standard.
Most strikes are called on fairly low turnout, it is true, and it's a shame that people aren't as engaged with the Unions as they used to be. Perhaps this is partly because in recent years the Union leadership has been completely unrealistic in its aims and grasp of economics; regardless, with so many people disengaged from Unions at the moment this legislation would have the likely effect of making illegal any future attempts at strike action. With the Unions' strongest bargaining chip no longer possible, the long-term consequence is that they have no power to fight any regressive changes by employers. That doesn't seem to be a good thing, although in practice I doubt the changes effected would be so dreadful for employees. But the principle is that workers must have a way to fight changes that they don't agree with, even if their fight is in vain (and on many occasions it certainly should be).
Low turnout never made PPCs, or MPs, or governments, or mayors, or local councillors, illegitimate -- at least, not in the eyes of our current democracy -- and I don't see why a turnout threshold should be applied exclusively to unions.