Unlike Ckcowl, I have no issues quilting through the logos. I feel if they are screen printed ink there is no issues but if they are the rubbery type transfers, like the kind commonly found in tourist traps or mall shops where they put the emblem on while you wait, you could have issues. Most high quality t-shirts like harley shirts and shirts made for concerts and special events are screen printed not the rubbery style transfer that cracks and peels over time.
Here are links to two where I quilted right over the tshirt logos. One was an all over working from the front of the machine that my friend pieced (and was also my first T-shirt quilt done on the LA), the other was a panto working from the back that I pieced. Both were double sided. I had no issues at all. I have done many others, these are the only two I have posted pics of.
Meg's T shirt quilt some firsts
Double sided T-Shirt quilt