I'm not a huge fan of the nukes, they're not really worth the trouble to locate, especially since you can only level up once you find all 10 nukes - and there were many instances when I completed the level with 9 nukes, not being able to find the last one.
So, I'm up to the sewers episode but I have only been able to level up once. Will this be a big problem to me later in the game? I'm currently playing on the hardest difficulty, and so far it's still going good for me.

No, it won't be a problem. :)
I think I only got the full 10 in two levels, possibly three. But you can happily beat the game without getting the nukes.

Cool, that's a relief to know, thanks man!

Sorry to take your relief but:
> When you find all the nukes on a difficulty, you'll get a reward when you
> complete the game. [...]
>
> Finding all the nukes on Hard will also give you the ability to fight the
> secret boss.
(somehow the quote tags don't work properly so I quote in good old BBS style)
From: Duke Nukem: Manhattan Project Nukes Guide by Marijn Kentie
http://www.gamefaqs.com/computer/doswin/game/473156.html
http://www.gamefaqs.com/computer/doswin/file/473156/17529
So while it is not necessary to beat the game, it is necessary if you want to see everything.