Nope, npn and pnp deal with transistors. You just need to make sure you don't put your cap in backwards or it can blow up. If your caps on the board have a polarity, buy another cap that has polarity. I'm confident in saying the caps are electrolytic, so you want to buy another electrolytic cap of the same uF value and a comparable V.
But yeah, if your cap is smaller and rated the same, by all means replace it with the smaller one if it'll save you some room.
And you can go smaller on the voltage in this application, but in general it's good practice to match both the capacitance and voltage ratings.