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I went back into Relic Passage in order to deal with the Surfing things, and I saw that a rock that I had previously plundered now had a hidden item again (a Shard). Are there are any other hidden items that regenerate, and if so where and what are they? Also, how often do they regenerate.

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There are 4 different rocks in Relic Path that give 1 shard each. Are you sure you have not gotten mixed up?? As far as I have found, Items only regenerate in the Hidden Grottos.

This source, Bulbapedia/ Recurring Items, mentions nothing about Relic Passage, staing only the Hidden Grottos.

These are things that can be found in the Hidden Grottos. After you have taken something from the Grotto, there is a 5% that you will find an Item or a Pokemon again every 256 steps.

All these items can be found in any Grotto.

Bold are hidden within the Grottos, so use the Dowsing Machine.

Damp Mulch
Growth Mulch
Stable Mulch
Gooey Mulch

Super Repel
Max Repel

Poké Ball
Great Ball
Ultra Ball

Super Potion
Hyper Potion

Big Mushroom

Rare Candy
PP Max

Red Shard
Green Shard
Yellow Shard
Blue Shard

These stones can only be found in specific Grottos.
They follow the same rules of regenartions.

Routes 2, 3 (dark grass), 5, 6 (near Breeder), 7, 9, Floccesy Ranch

  • Fire Stone
  • Water Stone
  • Thunderstone
  • Leaf Stone

Route 6 (Mistralton Cave)

  • Moon Stone
  • Sun Stone
  • Shiny Stone
  • Dusk Stone

Route 3 (pond)

  • Dawn Stone

Source: Bulbapedia/ Hidden Grottos

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Yep, pretty sure. I remembered to save (I always do) and I remember taking a Shard from that rock prior to this time. It isn't so far-fetched that we get regenerating hidden items. We had that with One Island in Gen III.
and the first link supports your last sentence. Also:

"In Generation V, TinyMushrooms will regrow, though they will remain invisible. Primarily, these are found on Route 6 and Route 12, but can also be found in Icirrus City in the winter. Additionally, a Pearl and Stardust will wash up on Route 13 or at Undella Town once per day. These may either both be found beside the Black Belt on Route 13 or on the very easternmost shore of Undella Town or one in each location. Another Pearl may be found periodically on Route 18 near the Battle Girl. It appears that the Lemonade found on the road on Route 9 will regenerate, but how often is unknown."

This is Gen V. Nothing about Relic Passage. Maybe they have not updated for Relic Passage...