Since the personnel doesn't know if a guest will take empty bottles with him at the end of his stay, simply removing empty bottles from the room can be considered theft.
I guess, in Portugal (or anywhere else on earth), the personnel will also not remove money found somewhere in the room; the code is to place the tip clearly visible on the pillow.
But how to clearly indicate an empty bottle as tip? Put it into the trashbin? Together with banana peels and other junk?
As long as there is no code for this type of tip, personnel would only remove bottles at the end of the stay.
Next, the guest makes the personnel do extra work to get the tip. Someone has to collect all bottles (paid working hours) and bring them to the next supermarket (for sure not paid). One bottle is 0.25€, minimum wage is ~9€, so one hour is 36 bottles minimum. Collectig bottles over a longer time might help against the last point, but supermarkets are not very pleased if someone comes to bring 300 bottles.
And finally, empty bottles are some kind of waste. Leaving waste is a weird kind of tip, even if its value is significant...
Maybe a few words about this deposit system:
There are the traditional returnable bottles. They are made of glass or of thick PET (one can not squeeze them), are collected in boxes (one might even buy a box of bottles), and will be refilled. Those boxes make them easy to handle from the producer to the shop, the customer and back to the shop and the producer. So, this bottles/boxes are preferred by restaurants, hotels and other gastronomy. The deposit on those bottles ranges from 0.08 to 0.15€.
Due to the low value, and since the bottles will just end up in the same boxes as the bottles from the hotel gastronomy, leaving such bottles in the roomis not a tip.
In 2003, a deposit of 0.25€ was introduced by law on all light PET bottles (one can squeeze them) and cans which contain sparkling drinks. (Yes, no mandatory deposit on the same kind of bottle, if it contains juice). The bottles are recycled, not reused. Therefore, most supermarkets today have machines where inserted bottles are crushed up to save space, and the customer gets a voucher to get the money back. The machines also count the bottles for accounting with the next stage in the return chain. The customer, however, should not crush the bottles, since the machine will not recognize them. So, one has a big pile of bottles, and has to keep then as they are, just for the machine to recognize and crush them... Since heat and cold in the car tend to squeeze the bottles, one often has to lift the lid of some bottles to bring them back in shape in front of the machine.
You see, this bottles are quite annoying, and this is why gastronomy avoids them. For the same reason, the entire handling might make them a loss as tip, despite the high value.