I may not be an "expert" in JATS but as far as I know, numbered sections in JATS are as follows:
<sec sec-type="intro">
<sec sec-type="methods">
<label>2</label>
<title>Methods</title>
<p>...</p>
</sec>
<sec sec-type="cases">
<label>3</label>
<title>Cases</title>
<p>...</p>
<sec>
<label>3.1</label>
<title>Case 1</title>
<p>...</p>
</sec>
<sec>
<label>3.2</label>
<title>Case 2</title>
<p>...</p>
</sec>
<sec>
<label>3.3</label>
<title>Case 3</title>
<p>...</p>
</sec>
</sec>
<sec sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<p>...</p>
</sec>
<sec sec-type="results">
<label>5</label>
<title>Results</title>
<p>...</p>
</sec>
<sec sec-type="conclusions">
<label>6</label>
<title>Conclusions</title>
<p>...</p>
</sec>
When I use the --number-sections command in pandoc nothing happens but by passing the metadata command chapters:true the output is like:
<sec sec-type="intro">
<title>1Introduction</title>
<p>...</p>
</sec>
<sec sec-type="methods">
<title>2Methods</title>
<p>...</p>
</sec>
<sec sec-type="cases">
<title>3Cases</title>
<p>...</p>
<sec>
<title>Case 1</title>
<p>...</p>
</sec>
<sec>
<title>Case 2</title>
<p>...</p>
</sec>
<sec>
<title>Case 3</title>
<p>...</p>
</sec>
</sec>
<sec sec-type="discussion">
<title>4Discussion</title>
<p>...</p>
</sec>
<sec sec-type="results">
<title>5Results</title>
<p>...</p>
</sec>
<sec sec-type="conclusions">
<title>6Conclusions</title>
<p>...</p>
</sec>
Hope it helped!
Kind Regards,
Tiago Manzato