Would any of you know if the town of Helgen was around in the 2E or can point me to any reference to it during this time period ? Would it make sense that this town was in existance during this time period ?

It's possible, but it's unknown. It's said that it was originally just a keep for the empire before it was a town, so it could have been around since the Empire entered Skyrim.

Helgen was a fortified garrison town for the Empire. Prior to the Oblivion crisis I think that there were probably more fortified legionairy posts that were probably destroyed and sacked. I expect that the war with the Thalmor and the more recent Skyrim civil war has prevented the funds to rebuild Imperial outposts. Plus funds would be more needed to rebuild trade and civilian settlements first. Helgen was probably built due to it's location back to Cyrodiil.

In in-book games it mentions Dawnstar as an Imperial garrison town which means the fort over looking the town was also an Imperial garrison which protected and used the port for trade.

Helgen may be a newer fortification built after the Oblivion crisis to replace many other derelict Imperial forts we see scattered across Skyrim.