does this means that bitrate shold be set to D* 9600
  when the parameter "D" is sent in the ATR ?

No.  The atr offers a set of possible protocols that the card can speak.
The terminal gets to choose among them by sending a pps request.  If it does
not send such a request, default values of F and D are used.  Those defaults
(372, 1) result in a speed of 9600 bps if you use the common 3.57 MHz clock.

If the terminal does send a pps, it gets to choose any F and D up to the
maximum supported by that protocol, as given in the atr.  See 7816-3
sections 6.6.3 and 6.5.2.

I think the max for Cyberflex is FI=9, DI=4, which gives you 55928 bps.  Or
maybe that's just the fastest that's compatible with a standard 550 uart.

I have never seen a card with internal clock so I don't know how those work.
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