"I would like to upgrade directly C9300-48T-E from Everest16.6.6 to IOS XE Gibraltar 16.12.7. Is there any upgrade path?"
No need for an upgrade path, you can go directly from 16.6.X to 16.12.X. Same if you go from 16.6.X to 17.3.X or 17.6.X.
Note that 16.6.X / 16.9.X / 16.12.X are already EOS/EOL and current recommended codes are 17.3.X and 17.6.X, see the document below.
Recommended Releases for Catalyst 9200/9300/9400/9500/9600 and Catalyst 3650/3850 Platforms
https://www.cisco.com/c/en/us/support/docs/switches/catalyst-9300-series-switches/214814-recommended-releases-for-catalyst-9200-9.html
"Will i encounter any license issue for the Gibraltar 16.12.7? will there be any issue with the compatibility issue?"
Not necessarily an issue, but you will need to implement Smart Licensing if you go to any code beyond 16.9.X.
For 16.12.X is called Smart Licensing:
System Management Configuration Guide, Cisco IOS XE Gibraltar 16.12.x (Catalyst 9300 Switches) | Chapter: Configuring Smart Licensing
https://www.cisco.com/c/en/us/td/docs/switches/lan/catalyst9300/software/release/16-12/configuration_guide/sys_mgmt/b_1612_sys_mgmt_9300_cg/cisco_smart_licensing_client.html
For 17.3.X and 17.6.X is called Smart Licensing Using Policy:
System Management Configuration Guide, Cisco IOS XE Amsterdam 17.3.x (Catalyst 9300 Switches) | Chapter: Smart Licensing Using Policy
https://www.cisco.com/c/en/us/td/docs/switches/lan/catalyst9300/software/release/17-3/configuration_guide/sys_mgmt/b_173_sys_mgmt_9300_cg/sl_using_policy.html
"I will use bundle mode which I will tftp upload to stacked switches, no boot system to the Everest IOS, then configure boot system to the latest Gibraltar. Will there be any issue?"
Those steps look good. If you go for Bundle Mode then don't forget to copy the .bin file to all Switches of your Stack. Also don't forget to do a "write mem" following your step of "no boot system to the Everest IOS" so the boot variable is cleared and then you verify the boot variable with "show boot system". This link below shows general steps for Bundle Mode:
Upgrade Guide for Cisco Catalyst 9000 Switches
https://www.cisco.com/c/en/us/support/docs/switches/catalyst-9300-series-switches/216231-upgrade-guide-for-cisco-catalyst-9000-sw.html#anc7
https://www.cisco.com/c/en/us/support/docs/switches/catalyst-9300-series-switches/216231-upgrade-guide-for-cisco-catalyst-9000-sw.html#anc19
However, as Leo mentioned, you probably do not want to go with Bundle Mode and instead might want to use Install Mode.
With Install Mode you get faster boot times and features such as ISSU (not available for C9200 / C9300 but for other C9000 Switches) and Software Auto Upgrade. And again, as Leo mentioned, this is the way to go, Install Mode for all these new C9000 Switches.
"I would like to upgrade Cisco C9300-48T by using Bundle mode. However, my current switch mode is install. Can I use Bundle mode to upgrade or i must use install mode?"
You can jump between Bundle Mode and Install Mode. However, as Leo mentioned, Install Mode is the way to go, Install Mode for all these new C9000 Switches. Link below shows a step-by-step example for the code update on Install Mode:
Release Notes for Cisco Catalyst 9300 Series Switches, Cisco IOS XE Amsterdam 17.3.x | Upgrading in Install Mode
https://www.cisco.com/c/en/us/td/docs/switches/lan/catalyst9300/software/release/17-3/release_notes/ol-17-3-9300.html#task_xpb_3tx_xkb
