Hi,
PS must be programmed to get PS-PL CLK available. This will be done by FSBL, which is generated by your XSA where these CLKS are enabled.
In case you use Linux, linux files must also be regenerated otherwhise Linux will disable them again.
SI5338 is not preprogrammed, to get SI5338 CLKs you need FSBL --> see Starterkit reference design
br
John