Brian,

Leaving the hops will not affect flavor. Primarily, hops impart flavor
to the beer through resins that are drawn out through high temp. If
anything, using the strainer only leads to a higher chance of
contamination as you add cooled wort to the fermentation bucket. If
you are going to use the strainer, make sure to dip it in your boiling
wort for 5 minutes to kill any bacteria before straining. I always
take the simple route and leave the hops in. They will be left behind
when your siphon to the secondary anyways.

John