I found a hacky solution that identifies the note number and the actual notes from the elements they use internally. This is not specific to notes created with marginalia and can therefore also affect other content in your document! The solution is also very specific to your requirements and is not easily extendable. If you think that your request would make for a good feature, please open an issue here.
The solution replaces the function super() with the function strong() in every box inside an align element. This will only target the number in front of the note since the inline number is only wrapped in a box but not in an align element. You can also use the function super() inside the note since the “body” is wrapped in a block instead of a box.
#import "@preview/marginalia:0.1.4" as marginalia: note, wideblock
#let config = (
numbering: (..i) => super(numbering("1", ..i)),
)
#marginalia.configure(..config)
#show align: it => {
show box: it => {
show super: it => strong(it.body)
it
}
it
}
#lorem(20) #note[hello#super[there]] #lorem(20)
Please make sure that the code examples in your questions compile without error, especially for the second example that actually shows your issue. The import of marginalia was missing as well as the actual creation of the note.