Couple thoughts for you.
1) The drain smelling is most likely coming from the first foot of the drain between the sink and the trap. I have a baby bottle cleaner that I use. Take the drain plug out run the brush up and down for 30 seconds flush with soapy water problem most likely solved.
2) As for the bathroom floor/shower problem. If she had moved out and not told you, you would have hopefully noticed this problem anyway and then would have fixed it regardless. Use the tenant complaint to your advantage when they start complaining about the inconvenience of a bathroom that is under construction. Try to work with them and have the work done when they might be out of town or something like that...
If you get on your horse you can redo an entire bathroom on a long weekend (3 day). I know this because I did one in a tenant occupied house myself one year over Labor day. She went out of town on Saturday morning and we were finished by Monday afternoon. You need to line up all your materials and workers ahead of time and do whatever break down possible before they leave, but it can be done. In your case you could offer ( you should have done an inspection before renewal, but anyway) partial credit on a hotel room if you want to encourage them to go on a mini vacation, or you can tell them to live with it until they are going away or their lease expires.
I'd just send a plumber over there and pay them for a quote to amend those issues. They probably won't quote the subfloor, but they'll likely diagnose the problem for you. You can use that info to form a plan and work with the tenants to appropriately address the issues.
Whether you think they withheld that info from you or not, you signed the lease to, so you have an obligation to reasonably respond to issues. Besides, a spongy subfloor will only get worse, it is in your best interest to fix it sooner than later.
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