The wait four hours message in the pop up box after replenishing in SH4 wasn't in the vanilla game. It was added by either RFB or TMO mod (can't remember which offhand), and even then the player wasn't forced to wait 4 hours before leaving port.
So it's not something "taken out," it's something that was never there to begin with.
I'm not aware of any mod that forces the player to wait that legnth of time, but there's nothing stopping the player from waiting a certain time before leaving port after a refit.
As far as the torpedo loading times are concerned I *thought* there was a mod that adjusted them, but can't find it and can't remember where I saw some reference to it.
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