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Allowing your distro to keep your kernel up to date is fine 99.9% of the time.
An older kernel (say anything more than a 18 months) usually has some documented flaws. If you patch the kernel around those flaws, running even ancient kernels isn't a problem. New kernels are better for new hardware, but when you have a working system, particularly on a server, there really is no need to upgrade the kernel.
Also, you do need to rebbot into the new kernel for the upgrade to take effect (this is generally not true for other components, except maybe glibc -- everything else you can usually just restart the affected application(s)).
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