The difficulty should be quite the same but that also depends on the boss fight.
The main advantage of playing as stealth character is that you may have much more ammunition for the boss fight left than a combat oriented player.
Combat based augmentations are an advantage in boss fights but they are not overpowered, so for example the Typhoon Explosive System won't kill bosses.
And also stealth based augmentations can be very useful for boss fights like the vision augmentation to see/track cloaked enemies (if the boss uses cloaking).
I consider the Dermal Armor augmentation as the most useful combat based augmentation for boss fights reducing the damage you receive and with the EMP Shielding upgrade preventing energy losses by EMP and electricity.
This upgrade may be also an option for stealth characters.
gaming.stackexchange.com/users/5136/Joe Scylla
I'm doing a stealth/pacifist run, and I don't feel that I've been overly disadvantaged by my augmentation choices.
In fact, some of the stealth augmentations are quite useful during boss fights.
Cloaking, in particular, is great: it's a lifesaver when the boss has you cornered and there's not adequate cover to sneak past him or her.
The biggest disadvantage I've noticed so far is that by not having any strength augmentations, I can't carry around a big cache of powerful weapons and the ammunition they require.
There's extra ammo available once you engage the boss, but it does make things tricky as you'll have to scramble for a new gun when you run out.
gaming.stackexchange.com/users/517/Mitch Lindgren
Once you realize that you can use Stun Gun on—basically—all the bosses, no.
It actually seems to be easier that way.
But invest in a damage-dealer for bosses.
Preferably a Revolver with the exploding ammo upgrade (which can be bought at the Detroit arms dealer).
Having Cloak is also incredibly helpful.
gaming.stackexchange.com/users/2799/Kiwi
I've only had one boss battle so far, but I did feel disadvantaged by my stealth-hacker build.
The problem wasn't so much the skills I'd chosen, though dermal armor and a typhoon would probably have made life easier (and longer).
The problem was my inventory: I'd filled it with a ninja's playground of delicate tools for artful, stealthy take-downs.
In the end I compromised my ninja code, dropping some subtle weapons and picking up a big old boomstick.
gaming.stackexchange.com/users/862/Feral Chimp
The first boss can easily be beaten with one EMP grenade followed by running around the room and throwing all the explosive barrels at him.
The whole time he still thought I was in the spot that I threw the EMP grenade from.
I took no damage and used no ammo besides the 1 EMP grenade.
gaming.stackexchange.com/users/12428/emp
For me the first boss went down pretty easy.
I had to adjust my play style, but I already had a few EMP grenades in the inventory...
so I went with EMP, then unload combat rifle clip into upper torso, run/hide.
Wash, rinse, repeat.
Also I tossed out a few frags since I knew I could use them on the fight.
The second boss fight was more confusing for me, I ran a lot, and died from tossing EMP grenades.
Then I figured we'd just play hide n seek, and the boss would have to find me by coming through my frag mine field.
That worked really well.
Thats as far as I've gotten.
I feel like the hacker build has gotten me a lot more EXP and Credits than my room mate who's taken a non-hacker, stealth based approach.
Before the return to China segment I actually had 15 unspent praxis points I had bought/earned by hacking everything in the game that I could.
At wich point I wound up buying dermal shielding, flash suppressant, lung rebreather, and anything I thought would help me out in the "Black Hawk Down" moment.
gaming.stackexchange.com/users/12328/NoFairFights
I think the only augmentations directly applicable to a boss fight are your dermal (armor) and Typhoon (your body is the weapon).
In my opinion what matters really is the same for all situations in life: What tools did you bring to the job?
For the first couple of bosses I recommend the Revolver with the explosive mod.
It can make fast work of them.
Later in the game, choose either the laser or plasma rifles as your anti-boss measure.
And if you pre-ordered and got the Explosive Mission Pack, you are in luck!
The grenade Launcher is so overpowered.
I took down Jaron Namir in 4 hits, and the final fight was really easy too.
The only downside to this weapon is that there are about 20 total rounds in the game for it.
gaming.stackexchange.com/users/9300/CyberSkull
Unlike the rest of the game, the bosses must be killed.
HOWEVER:
there's a stockpiles of weapons and ammo before each boss More importantly: for each boss there's a way to hack and activate turrets that will kill the boss for you.
gaming.stackexchange.com/users/113728/user1278519
I recently read a review of Deus Ex that said you could play a stealth character throughout most of the game, avoiding combat. However, they also said the boss battles were all strict run-and-gun fights.  I would like to play a stealthy character, but I'm wondering if the difficulty of the boss fights is going to be significantly higher if I don't have any combat-oriented augmentations.   Will I be gimped in these fights?   Do I need to throw a few fighting augs in with my stealth?
Are bosses harder as a stealth-based character?
gaming.stackexchange.com
<deus-ex-human-revolution>
gaming.stackexchange.com/questions/28574
gaming.stackexchange.com/users/816/sjohnston
Advantages include having more ammunition left over to fight the bosses. However, having no strength augmentations means you can't carry around a cache of weapons and ammunition. You can also use a stun gun on the bosses, making stealth mode less useful. It is an arguable point but specific strategies or workarounds can serve as a solution
There are advantages and disadvantages for a stealth character engaging bosses Specific strategies are being described that a stealth character can use There is a way to hack the boss fight despite the player being a stealth character