I don't think there's anyway to know, really, since we know absolutely nothing about his background. I've seen the movie about a million and a-half times (I showed it every year when I was teaching biology during my human genetics/biotechnology sections), and it never occurred to me to question if he was an in-valid. I've always assumed he was a valid for a couple of reasons:
1) Genes "eliminated" from the gene pool were those that were detrimental--myopia, ADHD, etc. In this case, the polydactyly of the pianist is not a detriment in the least. If the pianist had been born an in-valid with six fingers, I would suspect that the parents would have had the extraneous digits removed because such a condition such as that would otherwise be a VERY obvious sign of an in-valid birth if it wasn't specifically planned. I had always imagined the parents were also musicians and specifically engineered the pianist to have six functional fingers on each hand.
2) Unless the pianist composed the piece he was playing (which is possible), the piece had to be composed by a different six-fingered pianist because Irene specifically mentions that it can only be played by a person with six fingers. While the movie focuses specifically on those genetically engineered to be athletic and intelligent enough to journey into space, it stands to reason that parents who were interested in creating a child prodigy in music would also manipulate the DNA to enhance characteristics beneficial to that end as well. Perhaps in this new world, there are many six-fingered pianists.
3) The concert seems to be a well-publicized event attended by some mucky-mucks. I can't imagine an in-valid musician, regardless of how talented and capable he/she might be, would be allowed to play for such a group. In fact, early in the movie, Vincent stresses that in-valids aren't really given a chance to demonstrate their abilities and talents. If the pianist had been a true in-valid, he would probably have never been allowed near a piano because people would have assumed that he wasn't intelligent enough or talented enough to play it.