The SAT isn’t a substitute for Subject Tests, and AP tests rarely are unless the school specifically says it on their admissions web site. For schools that expect to see them, yes, you will be at a disadvantage.
It sounds like there are no options, so it is what it is. Hopefully the rest of the application portfolio can outweigh it.
fwiw, it’s much better to take Subject Tests before you’re already a Senior - typically at the end of the year in which you cover the material. My D took one as a Freshman and will take her second at the end of Sophomore year.