Ok this is going into an area where a lot of it depends on opinion.
First of all, yes, the samurai believed that the sword had a soul. The kami of the sword to be precise. This ties in with Japanese philosophy and religion. But this is not limited to samurai. A lot of this belief still lives on today in many aspects, and a lot of people still adhere to those beliefs. I myself have leanings towards those ideas. But that is personal, not fact. Meaning this is not something measurable or outwardly noticeable, and has more to do with beliefs and how those items (swords, knives, ...) are treated and used. It also does
not mean that the sword is considered is sentient being.
To give you a practical example: hand crafted blades are preferred by most Japanese chefs. When such blades have become unusable due to extensive sharpening over the years or decades,
some chefs send their blades off to a shinto shrine where some sort of cermenony is held, thanking the blade for its service, after which it will be ritually melted and cast to billets for forging a new blade. Healthy is not a word to describe physical health (like biological health) related to the kami.
It is more of a matter of... (I am going to be a bit vague here) in Japanese culture, there is a place for everthing, and everything should be in its place. Items have certain sizes and proportions that are considered 'right'. Meaning a shinken that is not healthy does not have the proportions or size that are considered optimal.
For example, I have a couple of Japanese natural sharpening stones. One of those is fantastic as a final polisher for straight razors (which is what I bought it for). It is of a quality that is normally reserved for sword polishing, with the price tag to match. The reason I was able to afford it was that it did not have the healthy size for a sword sharpening stone. It was not thick enough, compared to its length and width. It was still very expensive, but not the thousands of dollars that it would normally go for. It also did not have the 'right' color.
Additionally, Japanese sharpening stones (many traditional Japanese tools in fact) are not 'for sale' like you would expect in a western style shop. You don't go into a shop, plonk down some cash and say 'I want that'. The seller will not want to sell you anything if he does not have the idea that you can use the thing he is selling you. He may not even show you the really good stuff, and until he is convinced that the sale will not reflect badly on him, the conversation just keeps going round and round forever. Really
So to bring the example back to my stone: if -through lengthy conversation- I had not shown the seller that I had the skills to use that stone, and that I knew for which type of steel it was appropriate, there would never have been a transaction. Some people in Japan selling swords are still like that, and will not sell you a sword if you do not have the skills to wield it and a 'correct' attitude. Not everybody is like that anymore, but I do know stone sellers and smiths who would not sell you anything if they do not have the confidence that you will treat the things you buy properly and that you can use them. Relationships, experience and doing things right are still very important in dealing with traditional Japanese arts.
And finally, about throwing a sword: a sword is meant to kill or maim. Nothing else. If I try to throw a sword into your chest then that would not be disrespectful. I am trying to kill you, which is 'fulfilling' the role of the sword. That is never wrong.
The point is, throwing swords is difficult, and the chances of the sword hitting the ground or the scenery are high. If it hit something like stone, there is a risk of chipping the edge. This is bad because a chipped sword is a liability, and may not be fixable anymore. The 'not throwing swords' is more of a practical consideration. Throwing it for the purpose of killing is not an issue. Otoh, idly tossing your sword in a corner is considered
extremely disrespectful. See the difference?