A student who asked me to write a rec letter seems to have committed academic dishonesty in my class, what do I do?
You agreed to write this letter, and it is due tomorrow (!). Reneging on your promise would effectively torpedo the student's applications, as they are very unlikely to find another recommender on one day's notice. Given that you haven't even confronted them yet (much less convicted them), this would be altogether unjust. (Clearly, your dilemma would be very different if this incident had come to light a month ago.)
Given this timescale, I suggest the following:

Write the letter without any mention of your unproven suspicions.
Confront the student.
If the student confesses or is convicted, you could then consider contacting the programs to withdraw or amend your letter. This is a natural, just, and foreseeable consequence of A's decision to cheat in a class taught by their recommender.

One other thought: consider doing #2 ASAP -- you could ask the student if they are available for an urgent, important call regarding your letter of recommendation (that should get their attention). You can then confront them and also explain how this will (not) affect your letter. This conversation has a few possible outcomes:

You proceed as above. Indeed, I recommend writing the letter before having this conversation precisely so that your letter is not (even unconsciously) affected (as even innocent students may react poorly to serious accusations).
They withdraw their request for a letter. You certainly shouldn't pressure the student to go this route -- I wouldn't even bring it up. But it's possible the student will say that they prefer not to use your letter given the accusation; in this case, you should respect this.
They confess to cheating, at which point you can either rescind your offer to write the letter, or you can agree to write a letter that reflects this incident.

Note, if you do confront the student ASAP, you must be careful not to pre-empt the judicial process, nor to create an abusive, blackmail-like situation. Assure them that you have written a positive letter that does not mention your suspicions, and that you will not rescind or amend your letter until/unless they are formally convicted. Despite your best efforts, A will doubtless still be stressed; accusations of cheating are always stressful. But being transparent and giving A as much agency as possible is the best one can reasonably do under the circumstances.