There certainly are differences. Specifically regarding lemon there are differences not only in taste, because the lemon olive oil is flavored using the zest of a lemon, but also in acidity. Lemon juice is very acidic, olive oil is not. There are plenty of times where it is completely inappropriate to add an acid.
A better comparison would instead be lemon infused olive oil compared to olive oil and lemon zest. There would still be a difference, but it would be less noticeable. The infused olive oil has had more opportunity to capture the fat soluble flavor compounds in the lemon zest, however the flavor compounds that aren't fat soluble will be forever lost.
That is generally the trade-off when it comes to any infused oil. You will get lots of the fat soluble flavor compounds, but you will lose the non-fat soluble flavor compounds.
As for difference of use in the olive oil and lemon juice case, yes, definitely. You can't always add acids to foods. In the lemon zest case, apart from the slight flavor difference, there's also a texture difference. Of course, if you want something very smooth, pieces of zest wouldn't be a good thing. Apart from those though, not really.
All of these differences still apply both in uncooked as well as cooked preparations.
We had a very similar question about making your own garlic oil here:
Botulism, Garlic, Cold pressed Olive oil and mason jars
Oil is effectively an anaerobic environment, which promotes the growth of the bacteria and spores responsible for botulism.
However, these types of risks are common in home canning. Major factories producing canned or bottled goods are going to want to protect themselves against millions of lawsuits, so they are going to take steps to pasteurize (for lack of a better word) the foods before packaging them. Commercially-packaged infused oils have probably either been heated, acidified, or filtered to guarantee food safety.
On the other hand, the linked question above demonstrates that there are people out there who aren't taking the appropriate precautionary measures. If this oil came from a well-known company with a good track record then I would not worry (and you can always contact them if you are worried); however, if it came from somebody you've never heard of, and can't find any reliable information on - i.e. somebody who's making this stuff from home - then I might be a little more concerned.
If you trust the source, then trust the oil. Otherwise, you might want to try sterilizing it yourself; you need to either heat it to 250° F (121° C) or expose it to acid conditions. Neither of those things are really desirable; heating it can taint the flavour or even burn the oil depending on what kind of oil it is, and if you want to take the acid route, you basically need to to pickle it. But there you have it, that's what you can do if you don't trust the safety.
Best Answer
Per the University of Ohio Extension, yes, it does reduce the risk (emphasis added):
Still, reduce is not eliminate. The guidelines to not can or hold the oil for long term continue to apply.