Not really, as long as they have the right flare fittings on the ends. Braided will swell slightly and will make the pedal a bit more mushy as a result, but it shouldn't really be too noticeable.
I have semi-braided lines from the MC to the prop valve on my MJ, they came with the WJ booster and I liked the idea of having a flex section in the hard lines to reduce metal fatigue so I simply re-bent and flared the ends to match up with the MJ prop valve instead of the WJ ABS HCU.