In brief, Greek literature from the church fathers, to modern Greek Bibles, all reflect that Junia is an apostle. Information in the NET Bible note is inaccurate. Here is the short version,
When, however, an elative notion is found, ἐν (en) plus a personal plural dative is not uncommon (cf. Pss. Sol. 2:6).
In Pss. Sol. 2:6, the word episemos does not seem to mean "well-known to" but rather "with a mark." Here is the Greek with a literal translation,
- οἱ υἱοὶ καὶ αἱ θυγατέρες ἐν αἰχμαλωσίᾳ πονηρᾷ, ἐν σφραγῖδι ὁ τράχηλος αὐτῶν, ἐν ἐπισήμῳ ἐν τοῖς ἔθνεσιν
The sons and daughters were in harsh captivity
their neck in a seal, with a mark among the nations
Psalm of Solomon 6:2 NETS
Although ἐν plus a personal dative does not indicate agency, in collocation with words of perception, (ἐν plus) dative personal nouns are often used to show the recipients.
There also does not seem to be any word of perception in the Greek. It would help if the word of perception could be pointed out.