To be able to determine the entry-point of any attack, more information is required than just purely asking the questions above.
Security is a massive subject, covering a huge number of topics, configurations, environmental factors and most importantly site/server/software administration.
Initial questions to also look in to would be;
* Was the site, simply defaced? exploited by a shell?
* Was it a file inclusion exploit? File upload compromise? IFrame injection? DB compromise? Hosting/FTP Account access?
* Is Joomla! at the latest release?
* Was the Joomla! Security Guide followed?
* Are all your extensions up to date (and not listed on the VEL)?
* Is the hosting environment good/secure/well configured?
* Is PHP well configured and secured with something like Suhosin?
* Are there any 'unsafe' permissions on the directories or files?
You do have a known good backup? Don't you?
Exploits and compromises, can be effected many months ago and only exercised recently, look for modified files from awhile ago. Sites may have been online and available for many many months, years even, before they get attacked, just because it only happened two weeks after a change, this does not necessarily relate directly to the change. The possible fact that the site appears to be an online store, makes it more likely to be targeted (if it is a store based site, did you only recently switch to being a store, rather than maybe a brochure style site?)
This is not to say that your assumptions are definitely incorrect, and by no means am I defending the template or framework itself (I don't have enough knowledge of either to honestly say it is, or is not an issue) but I am just saying that there are many more factors to consider before jumping to conclusions that effect a large number of users and can possibly cause unnecessary concern for some.