"that are known" vs. "which are known"

In this clause

sexual assaults on crowded trains that are known as grinding.

they are defining the type of sexual assults that occur on crowded trains. I imagine from this sentence that there are multiple types of assults that go by different names. This seems like a good source on the topic: https://www.metro-magazine.com/10111994/sexual-crime-and-harassment-on-public-transportation-a-study

To answer your question, it is important to understand the difference between a defining and a non-defining clause.

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A defining clause (written with that or other pronouns, not with which, and written without commas)

One which gives essential information about a subject or object in a sentence.

A simple example: "The man that helped me is called Alex." Interpretation: There were several men there and one of them is called Alex. Alex helped me.

A more complex example: "I like to read case studies about startups that describe moments of failure."

Interpretation: There are many case studies out there. The ones that I like are the ones about start ups, more specifically the ones that describe moments of failure. In othe words, I don't like to read case studies that describe moments of success.

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A non-defining clause (written with which or other pronouns, usually not with that, and written WITH commas)

Non-defining clauses are just additional information. They don't specify and define, rather they inform.

Let's take the example from above:

"I like to read case studies about startups, which describe moments of failure."

In this case, the difference is that I like to read all case studies regardless of what kind of moments they describe.

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Why use non-defining clauses

Non-defining clauses are often used to add information which helps link the sentence to its paragraph, which helps flow and continuity.

Here is an example:

"I like to read case studies about startups, which describe moments of failure. Moments of failure is how you learn about the mistakes to avoid. By learning from mistakes, one is able to formulate plans that are more likley to lead to success."

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Coming back to your question

Mr. de Blasio called for stricter laws to curb sexual assaults on crowded trains that are known as grinding.

Just from the example you give, I would say that the main question to ask is this: Are they trying to address one particular type of sexual assault? Or are they trying to reduce all types of sexual assault.

In the above sentence, it sounds like they are focusing on this particular type of sexual assault and the measure they can take to reduce its occurance. I haven't read the whole article/paragraph so wouldn't know. If they are in fact only dealing with that particular sexual assault, it makes perfect sentence to use a defining clause. However, if they are veering the topic into another area or just adding additional information for another purpose and they are in fact generally discussing the topic of sexual assault, I would say it would have been better to use a non-defining clause.

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In the second example

For one thing, the modern traveller is often reminded of the Zionist and Israeli collective farms that are known as kvutzoth and kibutzim.

Here, I would agree with you because I have never heard of any other type of Israeli collective farms (I have been to Israel and read about its history). The fact that they are known as kvutzoth and kibutzim is just extra information.

I hope this answers your question.