i can think of 3 major explanations that cover the questions you're asking. there are some scholars of slavery who argue for or against specific explanations, while others are more interested in comparing how parts of each one may be useful. you can decide which "make sense" for yourself:

1. the point of the violence is to enforce the power dynamic between slaves & slavemasters to keep the system going. given how terrible the situation is (especially the racialized, transatlantic version), you could reason, enslaved people would surely flee & resist en masse. the function of all that gratuitious violence - much of which was specifically justified as punishment for resistance - was to send the message that "no, you can't get away" & "you have to do what i tell you, end of story". there is a lot of debate about how successful this strategy was, though.

2. if a slavemaster was wealthy enough, this level of violence could actually appear more profitable. if you use force to make people produce more cash crops faster, you can sell more & earn more money. & given that, as you said, violence & disease were killing people at very high rates, a plantation owner or another slaveowner could reason that it would actually be cheaper to just buy new slaves rather than spend a bunch of time & energy trying to "treat them well" only for them to die or run away in a few years. again, there's room to argue how effective this approach was at maximizing profit, but it was definitely a popular one, particularly in the Caribbean. (also, if you're a slave trader, any excuse to buy & sell more people helps you make money, even if it doesn't necessarily help other slaveowners.)

3. there are some people who argue that effectively, you're right - it doesn't make sense. rather than being a "rational" attempt at social control (option 1) or making as much money as possible (option 2), the key aspect of transatlantic slavery is just a deep expression of antipathy (basically, hate) for black people. some of the things scholars use to support this explanation include:

• the fact that whites & others engaged in enslaving & brutalizing black people even when it wasn't profitable. many slavery-based businesses were constantly losing money; much violence against black people wasn't against those who were "breaking the rules" or, for that matter, were even (legally) slaves or enslavable; policies like segregation were enforced even when they caused social problems or made economies less efficient.
• the fact that the victims of the transatlantic slave trade were overwhelmingly black, even though white europeans could have just done it to each other. there was certainly war, slavery, & forced deportation to the amerikas among europeans, yet they weren't massively enslaved in the "new world" - even though, by some calculations, it would have literally been cheaper & more efficient for major european empires to do that instead of going all the way to Africa for slaves.
• related to the above point, the fact that while at first nonblack indigenous peoples in the amerikas were enslaved en masse, many whites argued against & eventually shut down this earlier version of the slave trade, replacing it by expanding the already-established trade in black captives. this highlights how it's not just racism in general, but antiblackness specifically that motivates the system.

so those are the 3 big explanations: enforcing social hierarchy, maximizing profit (even if it may not seem like it at first), & just straight-up malice towards black people for no sensible reason. as i said at the beginning, some people sign up to specific "schools of thought" while others employ whatever they find useful, but if you're curious about any of them i can share some more in-depth sources.