You are forgoing several child-related benefits by filing as Married Filing Separately, such as the Child Tax Credit or Earned Income Credit.
You should prepare your return both ways, Married Filing Jointly and Married Filing Separately, to see which one gives you the best tax benefits, especially with the new tax law changes.
But yes, you are correct that you can only claim your and your dependent's medical expenses on your return, as you suggested, so you would only claim you and your son's expenses.
Here's a detailed article you may find helpful:
https://turbotax.intuit.com/tax-tips/marriage/should-you-and-your-spouse-file-taxes-jointly-or-separ...
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