I've always thought that, since he was sleeping in a coffin between CV3 and SOTN, it might be a nod to the incorrect but long and widely held belief that dead bodies continue to grow their hair and nails. Which I've seen referenced in a lot of old folk/pulp lore about horror and vampires. What actually happens in that case of course is that the body shrinks/shrivels over time making the hair and nails look longer.
More likely it was just a styalistic/art choice though. Lots of masculine heroes took a cue from Fabio and grew long hair in the 90s. Hercules, Duncan MacLeod, even Superman sported a mullet for a while. And you gotta admit that Alucard's hair looks fabulous flowing behind him.