If she is required to ask then that shows there is an issue all the way up in administration. A far easier, and less offensive way than looking at someones skin tone, is to ask, "Hello, how are you doing today?" and if they answer in a language other than English it is safe to assume they do not speak English.

Plus it sounds kind of racist that she would be required to only ask Asians if they can speak English.

Even if she's required to ask students if they can speak English, she can do it in a nicer manner and actually pay attention to the student. If they have spoken to her with no communication problems or have spoken in a language that is obviously not English, then I think that student knows how to speak English. Either way, it's still pretty racist, but the one way it could be worse is if she lengthened her words to help you understand what she is saying. That right there is the definition of a racist bitch.

Or just say, "we have to fill out a demographic form. What languages do you speak?"

Doesn't she have access to OP's academic record,if she went to school in America she probably had to take an English class at some point

In my district, in each student's permanent file, is listed the primary languages parents speak at home as well as each student's level of English proficiency (even if English is listed as the primary home language). Most schools and districts have this kind of data readily available on each student and a guidance counselor would definitely have access to these kind of test scores and information. Unless he or she misread or misunderstood something, I can't imagine why the guidance counselor would even need to ask that, excepting, of course, being an ignorant asshole.