scsi: ufs-msm: fix issue with setting the ref_clk enable flag

Fix missing update of ref_clk enable reference count when the
clocks are enabled and also enable shutting down the phy and
device during system suspend.

Change-Id: I7772cd87e0d0528ab5dbe6ea9f09e6d02c86f96c
Signed-off-by: Sujit Reddy Thumma <sthumma@codeaurora.org>