I would recommend against the rollers if you leave the kayak up on the rack for any length of time AND it's thermoplastic. I have a Necky Looksha IV (17.5', 57lbs) and have two noticeable divots on the bottom from my rollers. It hasn't affected the tracking at all, but looks funny and likely does affect the long-term durability of the material.
I've switched to the saddles now, but the damage is already done. A friend of mine that knows thermoplastics says I can fix it by filling it with rocks on a hot day (heat will allow the thermoplastic to loosen up and the weight of the rocks will eventually flatten out the divots).
It's up to you, the rollers make it very easy to get on the truck, but they will over time cause damage to the shape of the kayak. Personally, I'll probably stay with the saddles, keep the bottom of my kayak well waxed, and just muscle it up there - it's not much more work.
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