Okay...here's my take: I have sons (3 of them) and one daughter. My oldest son just turned 15...the next son will be 11 soon. At those ages, it is VERY awkward for them, especially once they start going through puberty. AND...they may or may not tell you how uncomfortable it makes them feel with you being in there. Personally, once my boys started getting bigger (even before puberty), I quit going in the bathroom for anything while they are in there. To me, it was just a matter of respecting their personal space and letting them know that I respect their need for privacy.
Sure, as a mom, your boys will always be "your little boys", but face it, they DO grow up! (The same is true for our daughters).
I'd suggest that you change their bath/shower times to some time other than when you need to get ready in the morning...or maybe someone's alarm can be set earlier so the bathroom is free when the next person needs to get in there. And hey, if you're still not sure how your son's are feeling...why not ask them? Let them know you aren't trying to embarrass them, you just want them to know it's okay to have their privacy when they need it!