I also think that you should use HPLC grade ethyl acetate. This will maintain your system's life. But as you said that you have not HPLC grade, then go with proper sonnication and degassing of mobile phase.
I agree with Joshi and Ansari. Don't forget a good filtration of the phase before sonnication/degassing. Just for confirmation, check for pH variations (should be minimum) of the ethyl acetate at different times.
Ethyl acetate if used in the sample preparation is usually evaporated and the analyte is reconstituted in the mobile phase before injection. So it will not harm the column