NP1 to NP2 the gain is 33% in power, the increment of NP2 to NP3 is low, in Shiki's case is 16.67%, NP3 Shiki would have 50% more NP damage than a Shiki NP1.
But if you really like Shiki and you aren't interested in Jeanne Alter next month, Shiki benefits more with NP3 than most servants, as her largest problem is her low NP attack an being NP3 makes her a more solid AOE, also she's an Arts servant which means you can spam her NP if you have Tamamo and Waver, so her 16.67% would be more noticeable because different buffs multiply.
Shiki full arts team with halloween princess and Chaldea mystic code:
Shiki NP2: 180,000 - 220,000
Shiki NP3: 202,500 - 247,500
Difference: 20k to 27k
Shiki no buffs, only with her own skills:
Shiki NP2: 55,318 - 67,611
Shiki NP3: 62,233 - 76,063
Difference: 7k to 9k.
So in an arts team, a fully boosted NP3 Shiki that NP spams her NP it's going to do 35k to 45k more damage than a NP2, which is decent for an AOE servant.
So it's your choice if think 35k-45k it's worth it.