
Yup Tom commited suicide (at least that's what been said here until now). And Henry blamed himself thinking his love confession to Tom was the reason he went to the war. Later Tom got post-traumatic depression as a side effect of the vicious war I guess. That's why he was in the facility being locked because he was not fit to be in outside world cause of his unstable and violent mental state. In the manga until now it's shown that Tom shot himself because he didn't want to hurt Henry and kill him by mistake.

That’s something Janet and Henry have been doing to keep Tom’s memory alive. Remember , Henry even built her that store so she can be the first to see Tom when he gets off the train when he finally comes home, even though they both knew he was actually gone. Now that they have both admitted it out loud, they purposely go on with the pretend, this way they keep him alive and don’t have to suffer the grief of reality.

As TheTenderVigilante explained it can be the mental satisfaction they r gaining by denying the fact that Tom is dead. Also it can be that there is much more to it as they just mentioned in the comics once that 'someone has to know about Tom to send Janet the letter'. So this can be a gateway for another plot. That's why I said that until now in the comics it's said Tom is dead(which most probably he is) and they r both just denying the reality to cope up with it.
i didn't understand tom's story :((
can someone explain it to me??..