Well, two reasons:
1. Because the units are still there and you are pretending they aren't. The "1" has units kg-m2. The equation should read E=1 kg-m2/t2.
2. The equation isn't describing the motion of a kilogram of mass, the piece you broke apart is describing the speed of light ("c" is the speed of light). So the 1m is the distance traveled by light in "t" time: time is a constant here, not a variable and you can't change that. So when you plug in m=1 kg, and d= 1m, t=1/300,000,000s and it all simplifies to E=9x10^16 Joules.
Science includes the implied assumption that the observed properties are real and there is nothing else to "concern with" or not "concern with". Beyond that, you're getting into philosophy, not science.