Is this a nod to new 52 or just a coincidence?

It is most likely a nod and not a coincidence, simply because there are too many such cameos by the number 52 in all Berlanti DC comic TV shows.

The number shows up in Arrow, The Flash and, as noted by the OP, also in Supergirl - and will therefore probably also pop up in the upcoming DC's Legends of Tomorrow.

In numerous episodes on all shows - it might even be worth a follow up question to determine, if actually in every single one - the number 52 makes its cameo appearance, either

• verbally, e.g. as a number in an address ("corner 52nd and ...") or - in Arrow Season 2 as the callsign of Officer Lance ("Delta Charlie Five-Two" = "DC-52"), or

• visually, as shown in the example picture. In Arrow, Channel 52 seems to be the Star City local news channel (the channel itself being a nod to the New 52), but it also appears on The Flash,

  at least one of their news choppers does, as Barry runs across its blades in the season 2 winter finale (The Flash - 2x09).

The characters themselves share some characteristics from their New 52 counterparts (while of course ignoring others to make it fresh and fitting for the medium).

[The New 52 is] the closest to our origin story and what we're doing. Grant "Barry Allen" Gustin in an interview

So while I could not (yet?) find a quote by anyone from the production actually confirming those numerous occurences to be nods, they are way too numerous to be conincidental, so the MythBusters would probably call it Plausible, I'd go further and say: most probably yes.