+1 for still having this problem.
I do not have Seasons. Therefore, it has never rained in my Sims game. 6 plants in the garden on the Legacy lot, planted on the first day or two of the Legacy. Founder is now about to die (97 days+ old). About a week into the Legacy, the Seasons update came out. Since then, for 90+ days, she has never had to water her plants. She has to fertilize, weed, can research, etc. But never has to water.
While she is gardening when I zoom in, the plants look like they are dripping with water. So the game clearly thinks they have been watered, even when they have not been for days and days.