number-depth ignored in _quarto.yml

By some reason, the sidebar resulting from the following _quarto.yml file displays the main section only, the actual value in number-depth (eg, 3) seems ignored:

project:
  type: website

website:
  title: "Patatin Patatan"
  
  navbar:
    logo: "HSILab.png"
    left:
      - href: index.qmd
        text: Home
      - about.qmd
      - citation.qmd
  sidebar:
    logo: "HSILab.png"
    style: "docked"
    search: true
    number-sections: true
    number-depth: 3
    contents:
      - section: "Introduction"
        contents:
          - 00_Abstract.qmd
          - 01_Approach.qmd
      - section: "Methods"
        contents:
          - 02_Methods.qmd
      - section: "Results VISNIR"
        contents:
          - 03_Quality.qmd
          - 04_ImageSequences.qmd
          - 05_IQMosaics.qmd
          - _051_SimpleReferencing.qmd
          - _052_ImageStitching.qmd
      - section: "Results SWIR"
        contents:
          - 06_SWIR.qmd
      - section: "Conclusions"
        contents:
          - 07_Conclusions.qmd
format:
  html:
    theme: default
    css: styles.css
    toc: false
    toc-location: right
    code-fold: true
    code-summary: "code"
    page-layout: full
    smooth-scroll: true
    anchor-sections: true

editor: visual

Resulting sidebar:

number-depth should not have an effect here. In particular, the documentation on Side Navigation does not list it as an available option. You could instead use approaches as described below.

Auto Generation

The sidebar can be auto generated by using a suitable directory structure. For your example with the three levels you could use something like this:

Directory structure

.
├── _quarto.yml
├── index.qmd
└── 01_Section
    ├── index.qmd
    ├── 011_Subsection.qmd
    └── 012_Subsection
        ├── index.qmd
        ├── 0121_Subsubsection.qmd
        └── 0122_Subsubsection.qmd

As stated in the documentation:

Navigation item titles will be read from the title field of documents.

Hence you could use the following contents for obtaining the result shown at the end of the answer.

_quarto.yml

Use contents: auto:

...
sidebar:
  style: "docked"
  search: true
  contents: auto
...

01_Section/index.qmd

---
title: "Section 1"
---

01_Section/011_Subsection.qmd

---
title: "Subsection 1.1"
---

01_Section/012_Subsection/index.qmd

---
title: "Subsection 1.2"
---

01_Section/012_Subsection/0121_Subsubsection.qmd

---
title: "Subsubsection 1.2.1"
---

01_Section/012_Subsection/0122_Subsubsection.qmd

---
title: "Subsubsection 1.2.2"
---

---

Manual generation

You can define a third level section and contents, e.g. such that your _quarto.yml contains something like this:

sidebar:
  style: "docked"
  search: true
  contents:
    - section: "Section 1"
      contents:
        - 01_ImageSequences.qmd
        - section: "Subsection 1.2"
          contents: 
            - text: "Subsubsection 1.2.1"
              href: _011_SimpleReferencing.qmd
            - text: "Subsubsection 1.2.2"
              href: _012_ImageStitching.qmd

---

Result