Are "Flow Free" puzzles NP-hard?
In the terminology of Nikoli Puzzles this is known as "Nanbarinku" or "Numberlink". The description does not always explicitly mention all squares must be covered, but this is indeed the case in all solutions I checked.

According to Wikipedia Numberlink the problem is NP complete, with reference: Kotsuma, Kouichi; Takenaga, Yasuhiko (March 2010), NP-Completeness and Enumeration of Number Link Puzzle, IEICE technical report. Theoretical foundations of Computing 109 (465): 1–7

I did not check the fine print.

Added. Following a comment from domotorp, Numberlink usually has an additional constraint. Indeed, quoting from Adcock etal:


  Our hardness result can be compared to two previous NP-hardness proofs: Lynch's 1975 proof without the “cover all vertices” constraint, and Kotsuma and Takenaga's 2010 proof when the paths are restricted to have the fewest possible corners within their homotopy class. 


Adcock et al. Zig-Zag Numberlink is NP-Complete, Journal of Information Processing 23 (2015) 239-245, doi:10.2197/ipsjjip.23.239