Possibly because he knew that the body would be found there on the subway car and he wanted it to look like a random mugging rather than an attack by a vampire, or possibly as an insult to her Watcher, the same as Angelus did to Giles with Jenny Calendar (that might have even been where Angelus got the idea) sort of a statement to the Watcher, who would have been the only one to see it, that Nikki wasn't a worthy enough opponent to even feed off of.
On the other hand, it might have been just the opposite, a gesture of respect to a worthy opponent. I can see Spike making a gesture like that. It's sort of poetic.
I would love to see that entire story presented in some format or other. So many questions are left unanswered, like who Robin's father was (the Watcher? That might explain why he took it as his responsibility to raise the boy. Or maybe Spike killed Robin's father in order to drive Nikki into a blind rage, making her more reckless and therefore a less dangerous foe. She certainly seemed more than a little bit pissed off at him in the subway car, much more so than Buffy ever seemed when she fought vamps.}
