Yes, they are different enough that some students do significantly better on one versus the other, so it would make sense to take both (or at least try old released ones of both for practice) in junior year to see which one the student is “ahead” on.
SAT subject tests cover high school level material, while AP tests cover more advanced level material that may be similar to material in college frosh level courses. For example, using the math tests:
SAT subject math level 1: high school math through geometry and algebra 2
SAT subject math level 2: high school math through trigonometry and precalculus
AP calculus AB: calculus, usually seen as equivalent to the first semester in college
AP calculus BC: calculus, often seen as equivalent to the two semesters in college
SAT subject tests are mainly used in admissions (though only a few colleges use them). Sometimes, they may be used for initial placement in math, English, and foreign language courses in college (though for math and English, usually just to place out of remedial level courses). AP tests are mainly used to give advanced placement (e.g. starting in calculus 2 or calculus 3 instead of calculus 1 after a high enough AP calculus score), though they may be considered in admissions.