As far as I know, if you have the RAM, it's okay, but if Emacs ever did hit really high usage before GC'ing, it might take a long time. I'm not sure exactly what Eli means; ISTM that if you have enough memory, it should be okay, but he's the expert here.
Having said that, I've used these lines in my init file for a while now, and it helps reduce startup time without making the changes permanent:
;;;;; Startup optimizations
;;;;;; Set garbage collection threshold
;; From https://www.reddit.com/r/emacs/comments/3kqt6e/2_easy_little_known_steps_to_speed_up_emacs_start/
(setq gc-cons-threshold-original gc-cons-threshold)
(setq gc-cons-threshold (* 1024 1024 100))
;;;;;; Set file-name-handler-alist
;; Also from https://www.reddit.com/r/emacs/comments/3kqt6e/2_easy_little_known_steps_to_speed_up_emacs_start/
(setq file-name-handler-alist-original file-name-handler-alist)
(setq file-name-handler-alist nil)
;;;;;; Set deferred timer to reset them
(run-with-idle-timer
5 nil
(lambda ()
(setq gc-cons-threshold gc-cons-threshold-original)
(setq file-name-handler-alist file-name-handler-alist-original)
(makunbound 'gc-cons-threshold-original)
(makunbound 'file-name-handler-alist-original)
(message "gc-cons-threshold and file-name-handler-alist restored")))