Three things:
1) If a shadow directly touches Neji he can break free by emitting chakra from his body, just like Kidomaru's web.
2) Let's say they both clash with a punch, Shikamaru won't be able to transmit chakra through the shadow of his punch to Neji because the chakra points in his arm are already affected and damaged.
3) When Shikamaru did this to Hidan, he had already a small shadow out, all he needed to do was extend it, Neji would notice this. And besdies, you're imagining a close-combat battled..if it gets close combat, Neji would just use one of his many Jyuuken techniques that if hit, Shikamaru wont be able to use chakra.