Aqua does not do its own spam filtering.
It syncs each folder independently of others, whatever's there on the mail server (in web mail) you'll get in the app.
"False positive" spam processing can happen, e.g. Gmail often errors on this side.
Please consider creating filters (message rules) in your mail provider's web mail (web site), hopefully they have an "action" to "never send to spam". Should be in their web mail (web site) under Settings somewhere. Look for "message filters", "message rules" or similar.