NA options

Currently b16a2 stock pretty much has travelled a few kms 30x,xxx(car acquired around 295,xxx).. just want to know if it's worth throwing a few bits in to give it some umph...

Option1:
Ek9 cams, gears, im, tb, fpr, f.rails, injectors + eventual tune + itr gb?

Option2
b16a head fully built
freshly machined
ported & milled
skunk2 internals
-titanium retainers
-valve springs
- sprng base kit
- skunk2 stage 2 pro series cams
includes new headgasket and intake manifold

Option3
Nothing and drop a b18c5/7 later down the track

Both options(1,2) can be had for similar price
Do I need to worry about my stock bottom end with either option for its age

Seeing as you've hit 300000km, the age of the block may be a issue for option 1 and 2. If I were you I would save the coin for a healthy c7 package instead of using your b16 as the base.

What kind of costs to rebuild oem spec bottom end b16?

Have you looked a doing an LS/VTEC conversion? This will net great midrange torque due to the long stroke while still maintaining good rpm.

Also Skunk2 Pro2 cams on a stock compression B series is major overkill.

Buddy Club Spec3, Rocket Motorsport M21x or M22x, Toda B are all good options for stock comp B series

no replacement for displacement.
i'd look at the b18 swap - especially if you can do the box as well

b20 vtec for sure
build the block (even mild build would be brilliant)
keep the head and you're laughing, maybe some head work if you're heaps keen.
if you're gonna drop some coin, drop it in the right places.