You may know where these hidden clocks and bottles are. But if you don't, I'll give you a hand. They will count in the long run, and you'll save yourself a whole heck of a lotta caysh if you find these instead of buying them in the hidden shops.
Clocks:

Hiyarika (Stage 3): Just below the Blackheart's warp.

Chaprun (Stage 5): Located in the middle of the "fountain" scene.

Sbadarian (Stage 7): In a hole in the "desert" scene. Highly crucial.
Red Bottles:

Sarcand (Stage 2): In the "crystal" scene. That has the shop in it. Shoot at the tallest crystal.

Sbadarian: In the same scene where the Blackheart's warp is located. It's in the middle of the three loops at the bottom.
Blue Bottles:

Bow Bow (Stage 4): In the "Inferno" scene with the shop in it. Shoot around and you'll find the bottle.

Fuwarek (Stage 6): In the opening scene. Left of the shop. A little strategy is to buy the red bottle at the hidden shop and then get the free-bee.