Not really, as every stage 2, 4, 6 give bombs on the midboss and 3, 5, EX/Phantasm for lives since the PC-98 games. Since you're going through stages 4 and 6 twice, you'll only get more bombs.
Actually that was only from MS to MoF (plus various fan games that use the same system).
SA just uses the same system for every boss phase, and the following games mostly do too (but with exceptions-- UFO's 1ups from stage 4 and Extra, TD's +1 life/bomb spirit from stage 2+ midbosses and +1 bomb spirit from all Extra phases, DDC Extra's 4 bomb/life parts if you capture the final midboss spell).
SoEW gives 2 bombs from the stage 3
boss, a bomb and a 1up from the stage 4 midbosses (other midbosses don't drop anything), and a 1up and a bomb from the stage 5 (final) boss.
LLS was similar to MS-MoF but had a second midboss in stage 4 that gives a 1up, with no midboss in stage 5 (and stage 6 has normal enemies that give both a life and a bomb).
(yay for random details that are mostly irrelevant to the thread)
And I agree, adding a few more point item extends would make sense to compensate for the additional stages. Technically IN gives extends every 500 after 9999 (probably code left over from PCB), so if the 9999 extend was somehow moved to 1500 or so, it'd work I think. Though this way does add an additional endurance aspect.