Will 12AX7 tubes in phono and line amp last longer than 12AU7 driver tubes ?

I would say keeping at least one 12AX7 and three 12AU7. 

When the 12AU7 in the driver circuit fail on one channel, I would say it is better to replace the 12AU7 for both channels.

Johnny

IIRC, 12AX7's have a higher output than 12AU7's, so that's a consideration, as well.

Talking vintage high quality tubes. The amp is VAC Avatar SE integrated.

How many spare sets should I have ?

i don’t have personal experience with your vac model, but in my travels with other vac gear, i would say kevin tends to run the tubes fairly hard in terms of biasing etc, so i would keep 3 good sets around ...