Umm… Per BFG; The Battle Barge only carries three companies and the Strike cruiser only One. This explains why the fluff mentions that the Strike cruiser may deploy it's entire compliment in just over twenty minutes! (The above mentioned Storm drop pod ) Also; I remember somewhere, (Might have been Tactica Aeronautica) that a Squdron of Thunderhawks consisted of 3 ships. (Remember, Thunderhawks are actually pretty BIG). This would fit with the Strike Cruiser carrying two squadrons: One of Thunderhawk Gunships and the other Transports. This would still allow the above mentioned Rapid Insertion/Extraction techniques! The Battle Barge per BFG only sports a Single Launch bay (Though it would be full sized and thus support three squadrons).
As per the Other poster's comment about SM always having superior tech: Battlebarges and Strike cruiser were designed and built during the great Crusade with the same engine designs of the ships of the time (Which are now what is typically considered the Chaos fleet.) An astute player will note that these ships are also typically faster than a comparable Imperial ship of the line. Also, The Battle Barge is very vulnerable to long-range lance fire once it's shields are down! Having played them in BFG I can tell you that they must be carefully managed to get close enough to an enemy to bring their Bombardment cannons and boarding parties to bear. In a running gunfight with another Battleship the Battlebarge typically gets pasted!
I'm pretty sure I mentioned the actual complements, but yeah, it does bear repeating. (There's probably plenty of extra space aboard the ships to carry more than the 3 and 1 companies fluff dictates, but it apparently isn't used for such in canon. Except possibly by Space Wolves and/or Black Templars, with their potentially larger, non-Codex formations).
And Thunderhawks… actually aren't all that big, compared to Starhawk Bombers and Shark Assault boats. Stormbirds were, but they were being phased out during the Great Crusade. A Thunderhawk is comparable in length to a Marauder bomber (which is of course Aeronautica), although it is chunkier (the Thunderhawk Transporter is, iirc, half-again the length). Per BfK, anything Aeronautica can be assumed to be roughly half the size of a void craft for the same role. If Sharks are bigger than Starhawks and have a smaller squadron size on that basis, then they're bigger than Thunderhawks.
There's no reason, of course that Thunderhawk squadrons couldn't be limited to 3 birds per squadron for some other reason, but it certainly isn't due to size limitations.
Also remember that per BfK (and even in BfG, particularly directly after release), the Launch Capacity of a particular bay was not the sum total of attack craft it could support, just the most it could launch at once. (Later revisions of the BfG rules limited the maximum squadrons of attack craft in play to a fleet's total Launch Capacity, justifying it as the max number of C3 links the fleet could support). Per BfK, a Launch Bay can fit up to 3 squadrons of small craft per point of Launch Capacity.
The Thunderhawk is listed as a Spacecraft in DW and is Size Massive Just like the Starhawk Bomber and Shark Assault bomber in BfK. This makes them (Very) approximately the same size. I've never really thought of the Thunderhawk as Aeronautica anyway!
As to the size of the Battlebarge I would contend that their is not a lot of unused space! Instead; I would instead suggest that a lot of that space is used for bigger engines and Lots of extra armor!