There appear to be multiple evidences that Bede had the heavenly witnesses verse.

First Grantley takes the negative approach:

The commentary on the Catholic Epistles by Bede (672/3-735) shows no trace of the comma, and only the faintest hint of a Trinitarian interpretation of verse 8. Interestingly, it seems that Bede was aware of the textual variant in nobis hcec unum sunt in verse 8, which he explains by means of a citation from Ambrose’s De Spiritu sancto.s8 In his homily on the Epistle for the first Sunday after Easter (1 Jn 5:4-12), Hrabanus Maurus (c. 780-856), archbishop of Mainz, likewise moves systematically through the passage in question but does not include the comma, a circumstance that suggests strongly that it was not in his lectionary. Like Bede (one of his principal sources), Hrabanus only hints at a Trinitarian reading of verse 8.59 The immediate context of the passage in 1 Jn is cited no less than four times by another Frankish bishop, Hincmar of Reims (806-882), who likewise fails to include the comma in every instance, even in the midst of his vigorous defence of the Trinity against the propositions of Gottschalk.60 More definite traces of the allegorical interpretation are to be found in a sermon on the same lectionary reading by Hrabanus’ contemporary Haymo, bishop of Halberstadt (t 853). Although the comma was apparently absent from the lectionary Haymo was using, he does imply that the three persons of the Trinity are "signified mystically” by the Scriptural verse, a conclusion he apparently reached through his reading of Eucherius. Interestingly, Haymo also says that the water, blood and spirit testify on earth, thus providing evidence of the uneven entry of the markers in calo-in terra used to distinguish the heavenly and earthly witnesses.61