It could cause change in retention time, but it won't change the polarity of acid/ion itself, rather than conditions of phase. The chromatographic retention/elution is based on two affinities of each compound: to liquid and to solid phase. When you change composition of liquid phase, you change compound's affinity to it, so the compound is eluted when affinity to liquid phase is greater than affinity to solid phase.

Quarternary amine salts are frequently more lipophilic and have smaller partial charge. This can sometimes help but they are also more expensive, more nutritious to microflora and harder to remove, which is why they aren't well-liked. Sensitive applications usually use tertiary amine salts, cause they don't influence as much.