Is it advisable to publish a paper in a Journal Issue edited by my PhD Supervisor? Or is it better to try to publish it somewhere else? My PhD supervisor is co-editing a Journal Special Issue, in a good journal, even if not top-ranking, with double blind peer-review (three reviewers are asked for the review). And I'm tempted to submit a paper (which fits with the topic of the Issue).

I've recently obtained my PhD, and I see that in order to apply for prestigious grants (such as the ERC grants) a requisite is "having produced at least one important publication without the participation of their PhD supervisor" (ERC starting grant).

In this case, it would be a solely authored paper (not invited by the Supervisor but submitted to blind review).

Is it worth to try and publish it there? When the paper is evaluated by a judging panel, will the fact that the Issue is edited by my supervisor be a negative factor?
It's not surprising this might happen. That your advisor is on the board (or equivalent) for a journal you might submit to is a situation often encountered. If you want to make sure no conflicts exist, ask your advisor to recuse himself from all decisions regarding your particular contribution. He might already have planned to, given the obvious conflict.