Hi Egol,
Interesting question, but difficult to answer. Could be a topic to ask on one of the Webmaster hangouts.
It all depends on how Google handles canonicals internally.
One possibility would be that Google considers the page from A that is syndicated on B not really as a page from B but a page from A. In that case, the links from that page would count as an internal link (A->A rather than as an external link B->A).
Another possibility would be that Google considers the fact that B is republishing the content from A as a kind of endorsement for A (in a non SEO world a site would only republish content from another site if the quality was really good). In that case, the links on the syndicated page would have value.
In both cases I would personally keep the links on the page. If you added them, it implies you think these links have some value for the visitor so taking them off wouldn't make much sense (unless your main goal was to add these links in order to optimise your internal link structure)
If you want to be on the safe side - if the links go to "commercial" pages, you could make them nofollow, if it's to other editorial content if would keep them as follow. I wouldn't omit the links - even when "nofollow" they could still generate traffic for your site.
Didn't found any "hard evidence" to support this, but we seem to have come in the stage where Google scared us so much about "bad links" that we start to question all type of incoming links.
Sometimes you just have to trust your gut feeling - if the link looks "normal" in the context (and adds some value for the visitor) I would stick to a follow link.
Dirk