Boolean algebra is a branch of mathematics frequently used in computer science. It deals with simple operations like AND, OR, NOT - which we also use in natural language.
In programming, two negations of a boolean variable cancel each other. You could express it in C++ as:
!!x == x
In natural languages, it's not the case. In English we don't use double negatives (unless it's intended, like in the famous song quote "We don't need no education" :) In Polish double negatives are used but don't result in a positive statement. For example, we say "Wegetarianie nie jedzą żadnego rodzaju mięsa.", which literally translates as "Vegetarians don't eat no kind of meat."
No matter what your native language is, in programming it's good to simplify things and so to avoid double negations. For example, if you design an API for your library and you need to name a configuration setting about an optional optimization Foo, it's better to call it "FooOptimizationEnabled". You can then just check if it's true and if so, you do the optimization. If the setting was called "FooOptimizationDisabled", its documentation could say: "When the FooOptimizationDisabled setting is disabled, then the optimization is enabled." - which sounds confusing and we don't want that.
But there are two cases where negative flags are justified in the design of an API. Let me give examples from the world of graphics.
1. When enabled should be the default. It's easier to set flags to 0 or to a minimum set of required flags rather than thinking about each available flag whether or not it should be set, so a setting that most users will need enabled and disable only on special occasions could be a negative flag. For example, Direct3D 12 has
D3D12_HEAP_FLAG_DENY_BUFFERS. A heap you create can host any GPU resources by default (buffers and textures), but when you use this flag, you declare you will not use it for buffers. (Note to graphics programmers: I know this is not the best example, because usage of these flags is actually required on Resource Heap Tier 1 and there are also "ALLOW" flags, but I hope you get the idea.)
2. For backward compatibility. If something has always been enabled in previous versions and you want to give users a possibility to disable it in the new version of your library, you don't want to break their old code or ask them to update their code everywhere adding the new "enable" flag, so it's better to add a negative flag that will disable the otherwise still enabled feature. That's what Vulkan does with
VK_PIPELINE_CREATE_DISABLE_OPTIMIZATION_BIT. There was no such flag in Vulkan 1.0 - pipelines were always optimized. The latest Vulkan 1.2 has it so you can ask to disable optimization, which may speed up the creation of the pipeline. All the existing code that doesn't use this flag continues to have its pipelines optimized.