Thanks for all the input guys. Seems a little pointless to rebuild using DB spokes right now and the nipples poking out seems like it won't be a problem.
Oh yes it will be a problem! Road bicycle tires run at fairly high pressures. The inner tubes do work against the tires, and against the liners, and against anything else they touch. This work causes friction and those extra long spokes will just add to the friction. The OP will experience flats because of the extra length. 3mm is quite a bit, when you have a thin piece of rubber being shoved and rubbed into it, for a long time, at very high pressure. Also...
With the higher pressures, forget the old rubber rim liners. They will distort into spoke nipple depressions on the newer style rims, once again, offering a perfect inner tube failure point - 36 of them, actually.
That's how I see it.