It's really situational depending how much you value the skip prize and what jokers you have.

Skipping is more valuable when:

• (like you said) you have a joker that triggers off of skipping like throwback
• you have jokers that decay like ice cream or turtle bean
• the prize is especially valuable to your build eg. a mega standard pack when you have Hologram
• you're past white stake and it's the small blind which now gives no base reward money

Skipping is less valuable when:

• you have a ton of money you could spend on stuff (not if you're trying to build up a lot of money for bootstraps/bull)
• You have Jokers that build up while playing like Spare Trousers and Burned Joker
• You have Jokers that trigger when you select a blind like Cartomancer
• You have Jokers that affect the shop like Chaos the Clown or Perkeo