Special abilities (SA) do not reduce the value. When you train a SA the price of the player stays the same because the player has no quality improvement.
What reduces the value is the end of the season and the player gets a year older.
edit: Sxrenity was faster.
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About the player development. In the lower levels (up to 7 or so) you are short on cash. Try to keep your team value moderate (some good fast growing youngsters, some middle age players up to 27 did the trick for my teams).
Later in the game your stadium and the youth academy (free 2* players you can get for free and sell for good money) help you to develop good talents. Furthermore the training center at a good level gives some green packs and player development is more effcicient in terms of stamina and training rate.
But please don't do my mistake and fast build the facilities at the first levels, you are only sad about the amount of tokens spend and you get again money problems. Build steady, try to win some trophies in the early stages and later in the game enjoy harder competition (managers who mostly know what they are doing and good player development).