Seki most likely does not pay attention in class. Though I wouldn't call any of it definitive, the manga actually throws a deluge of evidence that Seki is always playing. In contrast, I haven't seen him paying attention to class, so there's no evidence that he does.
- In the chapter 53rd Period in volume 4, Yokoi visits Seki's home and sees some of his prep work for his games. On page 134, Seki is shown holding two bags, one saying "1st Period" and the other "2nd Period". This implies that he brings a game every day for every class.
- In 55th Period in volume 4, we see how Seki does on two English tests. On the first, he gave up halfway and painted his desk plaid, which got him a 23 (Yokoi got 82). Yokoi's comments:
"Obviously! Your attitude towards class is reflected in that score!
Plus, during the test, Seki gave up right away and painted his desk
plaid. He should've scored even worse!"
During the retest, Seki used a myriad of toys to guess random answers for him. This time, Seki got a 95 and Yokoi got an 88. So from this chapter, it seems Seki plays even during tests.
- In 60th Period in volume 5, there's a parent visiting day, and we get to see Seki's mother. Seki's mother is immediately on guard, and launches rubber bands to knock away Seki's toys to stop him from playing around. His mother's preparedness and lack of surprise implies that Seki fooling around in class is a longstanding problem. The story heavily implies this with Yokoi's assessment of the situation:
"A rubber band!! Seki's mother shot him with a rubber band! [...]The
fact that she brought rubber bands with her... means his mom knows
that Seki's always goofing off in class!! So this isn't the first
observation day where he's played around. I can't help imagining...
The history of hardship suffered by Seki's mother!"
In spite of this, one could try to argue that it's simply impossible that Seki could get away with this every day all day, so Seki must pay attention to class at some point...
"Seems likely that he wouldn't always be playing around since the only
reason he gets away with his antics because he sits in the back of the
class. He probably hasn't always sat there, nor will he always sit
there in the future. But given the nature of the show and manga, I
doubt it is addressed." – Shaymin Gratitude, Nov 1, 2016 at 18:06
Due to the evidence I wrote out in the first part of the answer, I will eat my words. nom nom. While Seki's actions are more grounded than, for instance, Phineas and Ferb or Nichijou, much of his antics are highly improbable and beggar belief, so we're still dealing with a level of surrealism. Thus, we can't make this argument.
Though the comment is still valid in so far as things could change if the manga addresses this again. If I notice anything, I'll try to update the answer.