I think that we should respect etiquette and should be pushing ourselves in training; however, training responsibly also means maintaining health so that you can continue to train the next day, so that you can train without increasing the risk of hurting yourself or your partners.
With that in mind, only you can judge when and if it is time to take a short break.
When I started in aikido, I could not participate in a one hour class. I would have to sit quietly on the edge of the mat for 5 minutes at least twice a class because my cardiovascular fitness just wasn't up to par yet.
Four yrs later, at times I have to sit down during a long day of training (like at a seminar) if I just feel like I'm too tired to be safe--quite literally, that I will have a stupid and unneccesary accident like hitting my head on the mat during a roll or fall, due to fatigue.
And of course now that I am nursing a knee injury, I sit out any technique that would be unsafe or an aggravation.
Protocol is looser or stricter from dojo to dojo.
Where I train, if I am going to sit out a technique, I observe sensei's demo, then smile and shake my head "no" to prospective partners, and continue sitting quietly at the side of the mat. When sensei comes over to inquire he is satisfied if I just murmer my brief explanation. If it arises that I really need to take a break in the middle of practicing....well, if its just for a minute I use the "adjusting my dogi" strategy of bowing to my partner and sloooowly walking to the edge of the mat while I obviously fidget with obi, gi, hakama, etc, all the time doing slow deep breathing to recover my energy, then slooowly turn back, bow to my partner, walk back to the middle of the mat....if I really really need a break, I'll excuse myself from my partner with a bow, and sit at the edge of the mat.