The appearance rate of a Thunder Stone in Platinum is dependent on your trainer card's ID, with it being 1 with an even Trainer ID and 4 with an odd Trainer ID pre-National Dex.
The appearance rate functions like a lottery system where, for instance, a Small Green Orb with an appearance rate of 150 is 150x more likely to be found than a Thunder Stone with an even Trainer ID, or 37.5x with an odd Trainer ID.
The exact chance for an item to be selected can be calculated with its appearance rate divided by the sum of all appearance rates for any items available. The sum of the appearance rate is 1017 in both games pre-National Dex, which makes the chances for a Thunder Stone roughly 0.00098% with an even Trainer ID, or 0.0039% with an odd Trainer ID.
However, even with those rough percent changes, it's worth noting that,
Item rarity is more complicated. First, an item is selected from the appropriate list, weighted by appearance rate. Next, an attempt is made to place the item in a random spot on the mining grid. This attempt fails if the item would partially hang outside the grid area or overlap with a previously-placed item. If this happens, the process starts over by selecting a random item from the list again. Large items like the Root Fossil will fail to be placed more often than small items like the Heart Scale, and therefore they will be less common than their appearance rate alone would indicate.
With that taken into effect, it's even more unlikely to find a Thunder Stone, which is found in a 3x3 grid with the top left and bottom right tiles missing. In short, you should get a Thunder Stone from the Solaceon Ruins instead.
Underground - Item Appearances
