Analogy: Is it good practice for game developers to initiate the state of the game when a user plays it? User 1:"Woaw, I started the game near the end and finished it... uhm... kay", user 2:"I started at the start and had a whole game to play, nice!".
In that case it's very important , because it matters a lot.
If you are working with digital filters, then whatever you initialize the registers with doesn't really matter because it's crap anyways.
In this case it is not important.
In other words, it depends on what you are actually doing, if you got a menu system or some finite state machines then it usually matters a lot. It's 100% up to you, or the errors you receive, (I know Quartus can throw some errors if you don't initiate signals properly).
I'd recommend that you always initiate when the system resets, that's good design in my opinion, I'd hate to press "reset" that doesn't do anything when/if a system has crashed.
If I see that much of the routing resources are just for initiating states, then I'd acquire an FPGA with more resources, but that's just my personal take on it. But in the end, it's up to you and your future company and how you are going to use it. If you'd be more precise regarding your usage my answer wouldn't have been as general.
Had you presented something more along these lines:
I can initiate every state of my menu on my FPGA if I buy some FPGA with more resources, this will cost 10 more dollars per unit, I will be selling 1000 of these. So that's 10 thousand dollars, a relatively large sum of money.
Or, you don't initiate every state of the menu and whenever someone opens the menu random choices appear and you don't have to buy another FPGA. You're saving a relatively large sum of money.
"What should I do?", then I'd say upgrade your FPGA because anyone who uses your unit will not come back again for the next version you sell. So you may make a lot of money now, but lose 99% of your customers.
I say "FPGA" everywhere as a synonym of FPGA and ASIC, the problems are similar if not identical.