The former Brentford number one was missing from the squad to face the Trotters due to a thigh injury, which he picked up in the dying embers of the weekend's 2-2 draw with Manchester City.
Raya was seen limping through the mixed zone at the Etihad, although Arteta refused to disclose whether the Spaniard was one of his injury doubts before the third-round visit of Ian Evatt's side.
However, the Spaniard was unsurprisingly not named on the team sheet, and Arsenal confirmed on X that he was suffering from a thigh injury as 16-year-old Jack Porter made a historic start in goal.
The 2008-born goalkeeper became the youngest man to make a competitive start for Arsenal, who were also without the cup-tied Neto and third-choice Tommy Setford, who is nursing his own injury.
Arteta unsure of Raya availability for Leicester clash
Arteta was quizzed on Raya's status in his pre-match press conference, but the Spaniard was quintessentially tight-lipped, only confirming that he was still a doubt and his problem was muscular in nature.
"We don't know yet. He's got a muscular injury, yes," Arteta was quoted as saying by football.london, before also reacting to Porter's record-breaking evening in between the posts.
The 16-year-old surpassed Cesc Fabregas as the youngest man to ever start a competitive game for Arsenal, and he received huge encouragement from his teammates and the Emirates faithful on his landmark evening.
Porter was not too troubled in the first half, where Declan Rice and Ethan Nwaneri put the Gunners two goals to the good before the latter bagged his second of the night and Arsenal's third not long after the break.
However, Porter was denied a debut clean sheet when Aaron Collins skipped round him and tapped in a consolation for Bolton, and he also survived a nervy moment when an attempted pass cannoned off the leg of a Trotters player and landed behind for a goal kick.
After surviving that scare, Porter was largely a spectator as Raheem Sterling and Kai Havertz rounded off the scoring for Arsenal, and the 16-year-old's final act was to confidently claim a cross right before the final whistle.
Arteta reveals reason for starting record-breaker Porter
Arteta selected the Englishman over the slightly more seasoned 18-year-old Alexei Rojas, and he revealed that Porter's experience with England's Under-16 and Under-17 teams was a key factor in his decision.
"Jack has been training with us since pre-season and we were confident that he could do the role. Obviously, he plays in the national team. We've seen what he can do and we believe it was the right choice," Arteta added.
"We told him yesterday and he was over the moon straight away. I think he spoke to his family and they weren't prepared for that. It's a big step, it's a big occasion for them and I think they were nervous about it.
"But I think he reacted really well, he was really composed yesterday in training and today as well. His teammates really helped him as well on that. What an experience and what a way to break a record."
If Raya remains absent for this weekend's Premier League clash with Leicester City, Neto will be expected to make his debut in goal, but Porter could very well be on the bench for the visit of the Foxes.
Following the thrashing of Bolton, Arsenal were drawn away to Preston North End in the fourth round of the EFL Cup, and that tie will be played on the week commencing October 28.