We don't need to think of "photon torpedoes" as a constant unit of power, with the same destructive capacity no matter what ship fires them.
...Indeed, TNG makes it explicit that torpedoes have selectable yield and all, so even the hero ship torpedo is entitled to vary in strength of effect from episode to episode, or even from scene to scene.
But in this episode, "photon torpedo" is specifically used
as a unit of destructive power! As in, "1 NOMAD blast = 90 photon torpedoes".
Would you beam a shuttlecraft on board?
Again, in TNG, yes, you would. It's really quite convenient.
Of course, even in TNG, this would call for the shuttlecraft to cooperate. Shielded targets cannot be beamed...
But Kirk does give his logic for the decision. Having NOMAD aboard hopefully stops it from firing; trying to destroy NOMAD with the transporter and failing would be poor timing, as an angered enemy would be in a position to destroy Kirk's ship with one shot at that point. A few hours later, it would at least again take five shots!
Maybe it is logical to assume Nomad should be able to dish out more than it could take.
Traditionally, major war machines on Earth have been designed to be able to fight with their equals, with defense matching offense. But Kirk would see NOMAD as a minor war machine, for obvious reasons; those are classically built "unbalanced", typically biased towards offensive power because there isn't as pressing a need to protect the investment in them as there is to protect larger machines.