I will give a somewhat philosophical answer, which is no, in HoTT with LEM, pointed sets and sets are not the same thing. That is when you are working in HoTT, you always know when you are working with a set and when you are working with a pointed set and no confusion can ever arise from this situation.
What is true is that pointed sets and sets may be identified by an equivalence $e : \textrm{Set}_* \simeq \textrm{Set}$, which due to univalence gives us a path/identification $p : \textrm{Set}_* \equiv \textrm{Set}$. But paths/identifications in HoTT do not force us to treat the two sides of the path as indistinguishable, it says something more like "any construction we do with with pointed sets can be transported without loss of information to a corresponding construction on sets (and vice-versa)." If you work in a proof assistant for HoTT you will see that if you try to give a Set and say it's a pointed set, you will just get a type error, you would need to explicitly invoke the path.
If it makes you more comfortable to think in terms of models, we should think of these types as (infinity)-groupoids, in which case $\textrm{Set}_*$ is the 1-groupoid of pointed sets and base-point preserving isomorphisms and $\textrm{Set}$ is the 1-groupoid of sets and isomorphisms, and these groupoids are equivalent.
Edit: Also, you can remove the global assumption of LEM by replacing pointed sets with "sets equipped with a detachable point", i.e., pointed sets such that equality with the point is decidable.