I don't know how much and deep actual school kids in the US get in touch with Latin. In Europe you can choose it in many high schools and the use of it is common in mainstream media. For some areas of studies it seems to be a prerequisite.
In US literature, also scientific, it has to my opinion a kind of elitist touch, as it is in principal a dead language not spoken actively anymore and never was natively over there. I don't see Latin phrases quite often here despite a simple per se or use of acronyms like e.g. or i.d.. Of course, worst case would be a reader not noticing that it is Latin at all and supposing a spelling or formatting mistake.
What do you do when writing a English dissertation getting corrected by mostly European professors who you want to impress with eloquence/rhetoric quality ;) , but later also read by non-Europeans or used for applying for a job in an English-speaking country? Leave out all Latin phrases and use acronyms only? How common is it in English/US bachelor/master/PhD theses?