Hi fungi,
You've got some big names in DNN answering this post, and from a less known developer in DNN I would have to say if the responsibility for the system stands with you, be very careful. I myself have developed NB_Store (e-commerce) and one of my golden rules is to try and make sure it can upgrade to the next release. This is sometimes impossible, because we don't know what the next release of DNN will bring. But in my expreriance if the DNN module is correctly integrated into DNN then upgrades to DNN seem to be painless (Not always the case, but exceptions always break the rule). This leads me to think 4 things about your vendor:
1 - They've tested the application within the environment it exists in and believe no threats exists. (This is possible, depending on the structure, software changes and environment)
2 - They don't want to spend any money in testing an upgrade.(Hmm!!! say no more!!)
3 - They've change the DotNetNuke core in order to deal with your specific requirements (Not a bad thing if it's been dealt with correctly, hence upgrade may not need doing because the security issue are redundant or superceeded with their changes, but this would mean continual checking and could also be the reason they don't want to upgrade!!)
4 - The developer that did the original changes has left the company and they find themselves with a lack of DNN expertise (Could be a big worry!!)
In conclusion, you need to understaand why they can't upgrade? Their answers could give you the information you need.
Best of Luck,
Dave.