Do I need to let it dry under fume hood overnight when I am going to freeze dry it after hexane treatment

Here is what you ca do. You can put acetone on -20 C. When acetone is cooled add it to homogenized seeds (for example add 1 L of cold acetone to 0.5 kg of seeds powder). Mix it for 20 minutes in ice-salt bath. Then remove some acetone by decanting and filtrate remaining powder using Büchner funnel. What you get is acetone powder that you can keep at -20 C. Also you can repeat the hole process after filtration on Büchner  funnel. 

Check these publications:

Check this informative link on isolation of plant constituents:

http://www.slideshare.net/rahulbs89/extraction-of-plant-contituents

For complete de-fatting  of  the seed samples, dried seeds are advisable. Therefore, dried seed cake (powder) should be treated with n-hexane twice or thrice with fresh hexane with vigorous stirring complete extraction and allowed to settle. Each hexane soluble should be removed by decanting to obtain complete oil-free seed powder to use for protein extraction. Please note that  n- hexane is a standard solvent for complete extraction of oil.     

I agree with Dr. Rathod . You have to dry your seeds.