When writing about something done in another paper, should I write referring to the study itself or to the author? Should I write:

Click et al. (2018) through a linear regression analysis for the period 2000 - 3000 , carried out an analysis of the relationship between x and y. In the presence of structural breaks, They also included regressions for three regimes. 

Or shoul I write:

Click et al. (2018) through a linear regression analysis for the period 2000 - 3000 , carried out an analysis of the relationship between x and y. In the presence of structural breaks, it also included regressions for three regimes.
Referring to the authors of a paper (or group of papers) using the pronoun 'they' can certainly be done, but as always the journal's style guide will decide what you can do in a given paper. Just to drive home the point that it can be done, here are examples from two famous review articles published in Reviews of Modern Physics (arguably one of the most prestigious publication venues in physics). Both articles were written by native English speakers - one from USA and one from England - who both later were awarded the Nobel prize.

N. F. Mott's Metal-Insulator Transition (1968)


  The theoretical description given by Adler and others at Harvard is reviewed by Adler [15] at this conference. They point out that a lattice distortion occurs at the transition point,...


Kenneth G. Wilson's The renormalization group: Critical phenomena and the Kondo problem (1975)


  Schotte and Schotte (1971) have calculated the susceptibility χ(T) by Monte Carlo methods for the Coulomb analog. The violation of universality means that the value of TK they they calculate is unreliable because...


Referring to a given paper as 'it' also seems fair, but if you refer to "Click et al. (2018)" (i.e. a list of names) as 'it', well, it doesn't quite sit right. Still, a non-native speaker would probably get a pass on that one. Now, it gets worse if you refer to Click's previous single-author paper "Click (2016)" as 'it', however. I think most people would read that as a reference to the person Click, and a dehumanizing one at that. I think you should either avoid this usage altogether, or establish more clearly that it is the paper you're referring to. It probably is better to rewrite the sentence using a noun to make it more clear.

Actually, this is one of the big risks that comes with using pronouns: it might not be clear what they're referring to, even though it seemed so obvious to the author. In your first example, most readers will probably assume that 'they' refers to the authors. For a slightly more ambiguous sentence, however, they might think that 'they' refers to "x and y". In your second example, does 'it' refer to the paper "Click et al. (2018)", the "linear regression analysis", or the "analysis of the relationship"? Personally, I'd assume you meant the third option.