" So unless the Patriot Act can be turned into a Constitutional Amendment, the SCOTUS will not decide based on any special anti-terrorism principles."

No. They will decide however on  8 U.S.C. § 1182  in which Congress clearly delegated to the president the authority to suspend the entry of any aliens into the U.S. when he believes it would be “detrimental to the interests of the United States.”
Precedence has also been set by President Chester Arthur, who banned Chinese laborers from immigrating to the U.S. amid concerns of unemployment. Then, in 1924, President Calvin Coolidge signed the Johnson-Reed Act, which limited the number of immigrants coming to the U.S. while completely barring Asian immigrants. 
The SCOTUS  will rule in favor of Trump's EO much to the dismay of many.