Just like the better researchable Assyrians the Neo-Babylonians employed this as a proven tool to assert their control of the conquered lands and the remaining people there.   
Once the head of the snake is removed, it is no longer needed to crush that head?

The Assyrian policy of deportation is analyzed as 

> 1. punishment for rebellious behaviour; 
>2. liquidation of competing powers and weakening of potential centres of resistance; 
>3. formation of a layer of loyal subjects; 
>4. production of a homogeneous "Assyrian" territory; 
>5. acquisition of labour; 
>6. expansion of cultivated areas.
>
> — Markus Philip Zehnder: "Umgang Mit Fremden in Israel Und Assyrien: Ein Beitrag Zur Anthropologie Des 'fremden' Im Licht Antiker Quellen" (Beitrage Zur Wissenschaft Vom Alten Und Neuen Testament), Kohlhammer: Stuttgart, 2005. (p121–123)

And the main point for the Babylonians remained:

> As a political policy, the exile of leaders to distant locations was designed to weaken resistance in the colonies.   
> — PCB, p71. 

That the Neo-Babylonians were less radical in using this method compared to the Assyrians is self-evident: Israel disappeared into ten lost tribes, but Judah remained somewhat more 'unbroken' in terms of (material) culture and the majority of people living there. 

For comparison, Sargon boasted in his records that he had deported 27280 Samarians and destroyed the entire House of Omri. (Attested in this number range multiple times, eg (TUAT I/4, 378, 382, 383, 384, 385, 386, 387))

Whereas the bible itself says about the Babylonian deportation toll:

> 14 He carried all Jerusalem into exile: all the officers and fighting men, and all the skilled workers and artisans—a total of ten thousand. Only the poorest people of the land were left. ([2 Kings 24:14, NIV][1])

Of course, compare that with the number given in  Jer 52,28: 

> This is the number of the people whom Nebuchadnezzar carried away captive: in the seventh year, 3,023 Judeans; 29 in the eighteenth year of Nebuchadnezzar he carried away captive from Jerusalem 832 persons; 30 in the twenty-third year of Nebuchadnezzar, Nebuzaradan the captain of the guard carried away captive of the Judeans 745 persons; all the persons were 4,600. 
>
> — [Jeremiah 52 ESV][2]

The exact numbers may be up for speculation. "Tens of thousand" may be an estimate too high. But archaeology confirms that after Nebuchadnezzar went through, Jerusalem itself was for a time uninhabited, with [Mizpah][3] taking over the functions of capital for the new province.

To put the biblical account into more perspective, this time to get at the given numbers' reliability from looking at the 'historical and archaeological reconstruction' of the end of the exilic period:


|Biblical account Ezra 1–6| Reconstruction |
|-------|------|
| Cyrus issued a personal decree on behalf of the Jews, commanding the return and the rebuilding of the temple | Cyrus issued a general decree, which the Jews could take advantage of |
| |Temple rebuilding was a Jewish initiative|
| Sheshbazzar brought back temple vessels | Sheshbazzar was probably the first governor of Judah |
|A large group of 40,000+ returned under Zerubbabel and Joshua|The numbers returning were small, probably a trickle of individuals or small groups|


— Lester L. Grabbe: "The Reality of the Return: The Biblical Picture Versus Historical Reconstruction", (p292–308) in: Jonathan Stökl & Caroline Waerzeggers (eds): "Exile and Return. The Babylonian Context", Beihefte zur Zeitschrift für die alttestamentliche Wissenschaft, Volume 478, de Gruyter: Berlin, 2015. Table as excerpt)


That the Neo-Babylonians ended up deporting 'quite a lot' of Judahites in the end was the result of continuous resistance, rebellion and uprisings in the land, often in cahoots with other local powers, like the Egyptians. Something any strategic thinker would have wanted to minimize. So each time there was a rebellion put down, more people were removed from the troubled region. Better safe than sorry? This occurred in 597, 587 and 582 BCE.

— "Judah under the Neo-Babylonian Empire." in: Israel and Empire: A Postcolonial History of Israel and Early Judaism. Leo G. Perdue, Warren Carter and Coleman A. Baker, (eds [PCB]). London: Bloomsbury T&T Clark, 2015. p69–106. [doi][4]

— Hans M. Barstad: "Way in the Wilderness. The Babylonian Captivity of the Book of Isaiah The Myth of the Empty Land. History and the Hebrew Bible", Dissertation, The University of Edinburgh, 2010. ([PDF][5])


  [1]: https://www.biblegateway.com/passage/?search=2%20Kings%2024%3A14&version=NIV
  [2]: https://www.bibleserver.com/ESV/Jeremiah52
  [3]: https://en.wikipedia.org/wiki/Mizpah_in_Benjamin
  [4]: http://%20dx.doi.org/10.5040/9780567669797.ch-003
  [5]: https://era.ed.ac.uk/handle/1842/18676