The Northwest Ordinance didn't ban slavery in any states, but rather in the Northwest Territory, which is modern Ohio, Indiana, Illinois, Michigan, Wisconsin, and part of Minnesota. It was generally accepted that the federal government lacked the direct power to ban slavery within the bounds of a state and, with a bit more controversy, that it could not hold states to slavery bans if they arose from territories where slavery was banned previously. Illinois came fairly close to becoming an outright slave state shortly after statehood and did end up with an "apprenticeship" system which could get pretty close. That lasted into the 1840s.

The distinction here is that the Constitution gives sweeping powers to the national government to govern territories. In theory, Washington could do almost anything it wanted out there. Territories are often referred to as dependent polities with circumscribed rights, into which white men went to settle with the full knowledge that they would at least temporarily surrender some of the rights they were accustomed to in states. Those included the ability to choose one's own government officers, at least in the executive and judiciary, and the fact that Congress could veto any laws your territorial assembly voted through for any reason. In return, the nation paid the bills of the territorial government and managed it at a time when the local population of whites couldn't afford to do it on their own.

As to leaving slavery specifically to the states or territories to decide for themselves, what gets called popular sovereignty in the later antebellum, the idea doesn't become accepted as the one correct way to do things at any time in the antebellum. The Democratic Party, from about 1854 with the Kansas-Nebraska Act, makes the idea a test of party loyalty with fairly disastrous results for itself because so many northern voters disagreed. As late as 1850, the party could not get together a clear consensus in favor of popular sovereignty and so the issue was finessed by ambiguity in the case of Utah and New Mexico territories.

There were arguments for letting the locals decide about slavery way back, but they deal with existing slavery regimes. The Old Southwest (Tennessee and points immediately south.) made it clear that they would have slavery or they would likely switch their allegiance to the Spanish Crown. The national government lacked the willingness or ability to enforce any kind of slavery ban on them, so they were let have popular sovereignty by default. Largely the same thing, albeit absent the Spanish, happens during the Missouri Controversy. A challenge to slavery is rebuffed and slavery remains, but those are capitulations to an extant system rather than prospective solutions for the future. At the same time as Missouri was accepted as a state with slavery in perpetuity, the South voted for a fig leaf to support its northern allies by allowing a ban on slavery outside of Missouri in all parts of the Louisiana Purchase north of its southern line. In retrospect this became a point of precedent for antislavery Americans, but at the time it was understood as a basically worthless concession.

You do have southern radicals who will go out and say that Washington should keep its hands off slavery in the territories absolutely, on constitutional grounds, but prior to the 1840s they're probably not a majority in the section. It's when David Wilmot (D-PA) proposes his famous proviso to apply the Northwest Ordinance's slavery ban to the Mexican Cession that a really thoroughgoing constitutional theory contrary to that national power is articulated by John C. Calhoun and company. To make the argument, Calhoun had to suggest that basically every politician of significance including the men who wrote the Constitution and Calhoun himself had completely misunderstood the document and erroneously accepted national intervention on slavery.

Calhoun's argument is basically like this: The national government is not a thing in its own right. It is merely a joint agent of the states, absolutely bound to follow their dictates. As such, it does not actually hold territory but merely acts as a trustee for it on behalf of the states. Therefore, the small-c confederacy can do nothing which would impair the equal access to the territories and enjoyment thereof by the citizens of any state or group of states. Since banning slavery would effectively exclude southerners from the territories, it was completely unconstitutional and a grave injustice to boot.

At the time, this is news to almost everyone. Most Americans do believe the Constitution created a nation, not a league of states. They do consider Washington a government in its own right and to have powers not subject to veto by any states, as well as certain overriding powers vis-a-vis the states, albeit not so many of the latter. Calhoun's theory is part of a series of escalating demands from the white South for greater security for slavery and slavery's domination of the nation, which eventually prompts even fairly close allies in the North to declare the store is closed after they take a few too many beatings in the elections for their record of caving on demand to the Slave Power.

The ultimate of these is the proposal for a slave code for the territories, which is an issue in the election of 1860. The South has enough power in the Democratic Party to veto the nomination of any presidential candidate who will not sign on to resolutions in favor of an explicit federal slave code, which would introduce and establish slavery in every territory of the national domain. That's too much for the party's northern wing. When they hit an impasse at the convention in Charleston, SC, most of the South walks out. Attempts at reconciliation fail and the Democracy runs two candidates in the election of 1860. In the North, Stephen Douglas supports something like the regular party that didn't split. In the South, it's John C. Breckinridge on the slave code line and with the splitters.

The other guy from Illinois won in November on a platform of no new slave states and no new slave territories, period. South Carolina, followed by the other cotton states, found the win unacceptable and tried to quit the Union and take their land with them. When it became clear that Lincoln wasn't going to let them play "heads we win, tails you lose" with the results of a national election, most of the remainder of the South followed them out and the matter was litigated, ultimately, as the case of Lee v. Grant.

Sources

Most of this is standard antebellum survey fare. There are several good ones. For very basic nuts and bolts politics, I recommend McPherson's Battle Cry of Freedom. He covers it all in a chapter or two.

For detail, you can't beat Potter's The Impending Crisis. It's largely a history of the 1850s. But for a specific focus on the territorial question, the go-to book is Morrison's Slavery and the American West.

All of those begin in the 1840s and so can't link you up to the Northwest Ordinance or past crises as well as one might hope. For the long view, Freehling's Road to Disunion (2 volumes) handles the Southern end of things. I've yet to read an equivalent survey for the North (the North, as an interpretative frame, is less common than the South), but Fehrenbacher's The Slaveholding Republic covers the territorial question at some length.

Specifically for Missouri, the best (and nearly only) book is Forbes' The Missouri Compromise and its Aftermath. It's one of those books that always gets praise in the bibliographies.

For the Northwest Ordinance, Finkleman's Slavery and the Founders discusses its ambiguous history and dubious enforcement.