Where I'm presently contracting (non-aviation), there is a desperate drive to move all contractors off umbrella companies. So scared they are of this new Agency Worker Directive, that management has stated anyone not wishing to go Ltd can expect their contracts not to be renewed!
RYR BRK pilots own their Ltd companies but there is of course an "agency" involved. It would be interesting to see how this is interpreted with an Irish company employing and basing people from/in the UK. I would suggest you write to them for a clear answer.
By the way, this is more than just about holidays, companies would be forced to treat agency staff much more in the same way they treat permanent staff.