I was living in Lower Hutt then (and still do), so would have had a more ringside view of proceedings according to P+S canon.
A family joke at the time was no matter what happened, as long as the Griffins biscuit factory not far away from us in Gracefield stayed open to ensure a post apocalyptic supply of gingernuts we'd be fine
While realistically these days I wouldn't see Wellington getting more than one or two warheads, in the early 90's I did some pondering and came up with some extreme worst case MIRV target possibilities for Wellington:
1: Beehive. As a bonus even a smallish warhead here not only takes out the centre of government, but the port facilities, railyard, and urban motorway interchange to points north at Ngauranga as well.
2. Wellington airport. Wouldn't necessarily be rendered unusable from the Beehive strike due to Mt Vic being in-between. You might not be able to run strategic bombers out of the place but Hercs, Orions, and fighters can use it just fine.
3. Point Howard tanker terminal and Seaview storage tank farm in Lower Hutt. Major supply and storage point for POL for the lower North Island. Lots of industry and DSIR in the immediate area as well. Even if not directly struck they could burn for days/weeks.
4. Haywards Hill power substation in the Hutt Valley at Taita Gorge. Major link between North and South Island power generation and distribution hub for the lower North Island
5. Trentham Army Camp. Military target, nuff said.