There's a million of the 'why didn't they just' scenarios in Animorphs, especially towards the end.
Why didn't they just kidnap Tom? Someone mentioned that the Chee couldn't replace him because it results in a Yeerk death, but they replace the Animorphs all the time and hundreds of Yeerks, Hork-Bajir, and Taxxons are killed in the process. So that's a moot point. In book 31, Tom is isolated with Jake in the mountains with his family. Away from the Yeerk forces. Bring the gang, tie him up in the woods, have someone morph him so the family doesn't get suspicious. Done. Easy.
The biggest one that bothers me is the Yeerks being able to morph. Because it's the host body that's morphing. The presumably unwilling host, which the Yeerks will have to leave every 3 days to feed. So now you have tons of unwilling humans, with the power to morph, and they can't fight/escape from the Yeerk pool? What!? The animorphs have been infiltrating, fighting, and escaping the Yeerk pool the ENTIRE series, and there are SIX of them! And now hundreds of humans with access to birds, leopards, etc can't make it out of some measly cages?
For that matter, why even keep the human hosts at all!? Just aquire your human host, then kill them. Now you have able bodies, and less humans to fight against. Not that there's any reason to fight anymore, because.. NOW YOU HAVE ABLE BODIES, aka the entire reason the Yeerks are an issue in the first place. The whole 'Yeerks can now morph' thing was handled so poorly it was almost cringe worthy. Not to mention, they could have aquired and morphed their own Hork-Bajir, which the Yeerks themselves describe as basically being the perfect host body, able to fight as well as being dexterous enough to build things with. So I can totally see why, given the ability to morph, they would choose a lot of birds instead. Hell, they all could've acquired Visser One and went around in Andalite morphs. We've already seen that an Andalite is more than a good match for any Earth animal.
Why didn't the animorphs use Dracon beams? The only instance I can think of in which they did was when Marco fried a helicopter while protecting the governor. There's tons of times where the Animorphs get a hold of them and they just toss them away. Why not keep them? Same for the Hork-Bajir! For god's sake, they've 'raided' hundreds of Yeerk outposts by the end of the series, and yet when the Yeerks attack they defend the valley with sharp sticks! Are you kidding me!?
And why are they in a valley in the middle of nowhere anyway? Once they free the governor, they have military backup. Uninfested, informed military personnel. Instead they live in the woods with little shelter, rather than move to a secured military compound. Continue to defend with sharp sticks and holes dug into the ground, instead of anti-aircraft guns and artillery shells.
But at the end of the day, I guess the only answer that makes sense is that they are kid's books. All the bad guys have to be horribly stupid and have terribly bad aim because if they didn't, they should've fried the Animorphs in the first book and continued to take over mankind.