TL;DR: Because Jonas' plan is to make the boys angry enough to do something stupid - he isn't trying to disarm them. In fact, he wants them to be armed so they can destroy their own good standing with the townsfolk.
Why does Jonas ransack the cabin?
He wants the boys to get angry and lash out. However, he wants it to look like local kids ransacked the cabin, because he would rather the boys not know that he had figured out that they were gunslinger. He also doesn't want them to be sure that Jonas and the Big Coffin Hunters were responsible for destroying their cabin.
Remember, when Jonas first spies on the boys and finds the guns, he and the boys are still "playing castles", and neither side wants to "peek" around the "hillock" yet. That is to say, Jonas doesn't want the boys to know he's onto them, and the boys don't want Jonas to know that they know he's onto them.
He went to one knee and used the blade of his knife to pry up the board which had creaked. Under it were three bundles, each swaddled in dark strips of cotton cloth. These strips were damp to the touch and smelled fragrantly of gun-oil. Jonas took the bundles out and unwrapped each, curious to see what sort of calibers the youngsters had brought. The answer turned out to be serviceable but undistinguished. Two of the bundles contained single five-shot revolvers of a type then called (for no reason I know) “carvers.” The third contained two guns, sixshooters of higher quality than the carvers. In fact, for one heart-stopping moment, Jonas thought he had found the big revolvers of a gunslinger— true-blue steel barrels, sandalwood grips, bores like mineshafts. Such guns he could not have left, no matter what the cost to his plans. Seeing the plain grips was thus something of a relief.1 Disappointment was never a thing you looked for, but it had a wonderful way of clearing the mind.
- Wizard and Glass, emphasis mine.
Why did Jonas leave the guns?
If he stole them, the boys would know they'd been exposed. The mere fact that the guns had been discovered would prove that the cabin was ransacked by someone a lot smarter than local kids - someone like the Big Coffin Hunters.
Of course, the boys are smart enough to see through Jonas' ruse - Jonas wants it to look like the cabin was ransacked by local kids, but even he doesn't fully expect the boys to fall for it:
He rewrapped the guns and put them back, put the board back as well. A gang of ne’er-do-well clots from town might possibly come out here, and might possibly vandalize the unguarded bunkhouse, scattering what they didn’t tear up, but find a hiding place such as this? No, my son. Not likely.
Do you really think they’ll believe it was hooligans from town that did this?
They might; just because he had underestimated them to start with didn’t mean he should turn about-face and begin overestimating them now. And he had the luxury of not needing to care. Either way, it would make them angry. Angry enough to rush full-tilt around their Hillock, perhaps.
- Wizard and Glass, italics in the original.
What is Jonas hoping the boys will do?
Attack the oil tankers. They'd be less likely to do that if they didn't have their guns:
“We’ll start moving the tankers soon, whether the brats come or not. At night, and two by two, like the animals going on board Old Pa’s Ark.” He laughed at this. “But we’ll leave some, eh? Like cheese in a trap.”
“Suppose the mice don’t come?”
Jonas shrugged. “If not one way, another. I intend to press them a little more tomorrow. I want them angry, and I want them confused. Now go on about your business. I have yon lady waiting.”
- Wizard and Glass, emphasis mine.
Is this the last time Jonas checks on the guns?
No.
Jonas goes back again, later in the story; by then, everyone knows what's up, and he does destroy Cuthbert and Alain's guns. Roland's guns, however, have been relocated:
When they were out of sight, Jonas went into the bunkhouse, pulled up the board which concealed their little armory, and found only two guns. The matched set of six-shooters with the dark handles — Dearborn’s guns, surely— were gone...
Jonas’s hands went to work, disassembling the revolvers Cuthbert and Alain had brought west. Alain’s had never even been worn, save on the practice-range. Outside, Jonas threw the pieces, scattering them every whichway.
- Wizard and Glass, emphasis mine.
Conclusion:
As long as the boys and the Big Coffin Hunters were playing castles, and no one had peeked around their hillock yet, both sides were reluctant to make the first move. So Jonas trashed the cabin, and although he looked for the guns to confirm that the boys were gunslingers (or, in Alain and Cuthbert's cases, gunslingers-in-training), he knew that stealing the guns would expose him and let the boys know he was onto them.
However, once the final confrontation was inevitable, and it was clear that the boys knew what Jonas and his men were up to, Jonas finally felt comfortable destroying the guns. By that point, he had nothing to lose by doing so.
1Although Jonas thinks Roland's (aka "Dearborn's") guns are true gunslinger weapons, he only thinks so for a moment, and quickly realizes that, while they are higher quality than Alain and Cuthbert's guns, they are only apprentice revolvers:
In fact, for one heart-stopping moment, Jonas thought he had found the big revolvers of a gunslinger — true-blue steel barrels, sandalwood grips, bores like mineshafts. Such guns he could not have left, no matter what the cost to his plans. Seeing the plain grips was thus something of a relief.
- Wizard and Glass emphasis mine.
