probably not if you are talking about a power surge after the lightning strike. IF it was a direct hit, then the pickups would be nowhere to be found. Your amp however may be damaged by a power surge
The bass was plugged into a bass pod and the pod is destroyed But the output of the bass is far lower than it was before. Just wondering if this could have been caused by the lightning strike that killed the pod and my tuner?
It is unlikely. Pickups are wire wrapped around magnets which are a lot tougher than active electronics. If they get too hot they could melt or short windings. Surges in the electrical systems usually kill active electronics though.
What kind of pickups are they? Can you measure their resistances with an ohm meter? (You may have to unsolder the hot leads heading into the pots to make the resistance measurements). If the resistance measurements check out, you are OK.
If both pickups sound the same volume wise, there is probably nothing wrong with the pickups. The liklihood of both of them failing the same way is not high.