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.