Have not had any "official" personal experience with Bujinkan
, but I have had 2 students who studied this form of Ninjutsu prior to Aikido training and both were told by their prior instructors that if they could not find a Ninjutsu school, study Aikido.
From my experience with those 2 guys, there was a slight problem with separating the 2 philosophies and learning to relax a bit, but in the end they turned out to be pretty good Aikidoka.
So from my limited experience I would tend to say Yes, they should complement each other pretty well. However, it may depend on both your Bujinkan sensei's particular way of teaching taijutsu and your Aikido sensei's approach to Aikido. I think the practicality and resistance focus of our Aikido style made things easier for those guys honestly.
Generally though, I think one should have a sound foundation in the basics of any art before attempting to learn another.
Just my personal view is all.