yes. They will sound different since the hum cancelling will remove parts of the noise that is part of the overall sound of the single coil it could be a very tiny amount, it will still be heard imo.
The humbucking will usually sound rounder and smoother, with less highs than a single coil, like the Sadowsky hum cancelling and the single coils sound very different from each other.
You are talking about a regular "side by side" humbucker like you see on guitars. This is also the arraignment in many soapbars.
Split coil humbuckers, like on P basses, and on some jazz style pickups are different.
On a side by side humbucker, the string is being sensed by both coils. Each coil is electrically out of phase with the adjacent coil, but it is magnetically out of phase as well. This brings the signals from the two coils back in phase as far as the picking up the string is concerned, but noise, which appears in both coils with the same phase, is canceled out. The strings are not canceled out, because of the opposite magnets. However, since the two coils are close together, very narrow harmonics are somewhat canceled, and you loose some highs compared to single coils. The two close coils also reinforce the lows and mids, so humbuckers tend to have a fuller tone.
With split coil pickups, such as a DiMarzio Model J or Ultra Jazz, each coil only pickups up two strings, so none of the strings are sensed by both coils, so in essence you have two single coils next to each other.
The other style of hum canceling Jazz pickup has one coil stacked on top of the other coil. In this case they sometimes cancel some of the low end, but not the high end, and can be on the thin side. To get around this, they are often wound with more wire than a regular single coil. EMG J's are stacked, as some others.
But anytime you change the size of the coil, or the amount of wire on the coil, it will sound different. So they can get these pickups close to the original, but they often sound a little different.
Bass Player Mag reviewed some of the Nords, and said the hum canceling vintage style J sounded like the real thing, so it can be done.
You can also make regular side by side humbuckers that sound like single coils.
but then those DiMarzios have a very hot output, I've been using them for a while now in rock. 
and jumped on the humcancelling part
