For a bigger design, the larger delay of clock tree is inevitable,
but it doesn't matter, the most critical issue is skew, not delay.
For SE CTS, if it cannot meet the minimum skew, it must increase
the delay.
If you have inhouse clock tree design rule (the rule must be
enforced by some inhouse tool to check it). You can split your clock
tree into subtrees then do the highest level by "hand", if you don't have
the rule, you better do everything by tool.
by the way, which version of SE/CTS you used? i don't know
the performance of latest release, but the one in SE5.0/5.1 is not good
for bigger design. You may compare with Astro or Celestry's tool.