I have Hydra widget platform installed installed on my N9 from Ovi store. It's the latest version from the (no longer updated) store. I don't have NeilDK's version of Hydra (the totally unrelated pentester app) from openrepos installed. However, when I try an apt-get update, I see that there is an update for Hydra widget platform available (there isn't) and then it appears that the package manager is trying to update Hydra (widget platform) with Hydra (pentester). Is this even possible? Just having the same short package name shouldn't confuse the package manager, right?

It appears that, yes, in the Debian package management scheme, a package name conflict is resolved by preferring the higher-numbered version. Possibly apt preferences can help prevent one hydra from trying to upgrade a different hydra, but it doesn't seem to be a way to have both.

Anyone know a way?

Do you still have the .deb for Hydra-widget?
If so you could e.g. install Hydra-pentester, then unpack somewhere with dpkg-deb Hydra-widget and then manually copy the extracted installation tree to your system.
Of course it's up to you to insure that no file gets overwritten due to having the same path+name.

was this cordova based project opensource ?

No, doesn't appear to be.