I only looked at one of your proposed parts, the Murata LLL153C80G105ME21. I compared it with a same-value part in a larger package (GRM21BR71E105KA99#, 0805 size), the key improvement is in the available voltage rating. The 0204 part is rated for 4 V, while the 0805 part is rated for 25 V.
Even if your application only applies 4 V to the cap, take note of the capacitance change with applied voltage charts. The value of the 0204 part will be reduced to a bit above 30% of nominal (e.g. 0.3 uF instead of 1 uF) with 4 V applied. The 0805 part will still be at 95% of its nominal value with 4 V applied, and only loses about 45% of its value at 25 V applied.
So the smaller part can be used if you can accept its reduced temperature range, but its value will be reduced to just a bit more than the 0.1 uF value that has been typically recommended for use as the near-chip bypass capacitor over the past decade or so. If you really want 1.0 uF of bypassing, you'll still have add some larger parts in parallel with the suggested 0204 part.
On the other hand, if you can live with the low WV rating and you use this part in place of the "traditional" 0.1 uF 0402 part (in parallel with additional larger-value caps), you will gain a 3 - 4x increase in effective capacitance, so that is a substantial improvement.
Also, in a high-reliability application, you may want to use a package at least one size up from the minimum needed for the capacitor value and WV you are using. The smallest available size is pushing the limits of what the manufacturers can do, and can have reliability issues.
It is a matter of history, sadly. Capacitors where built well before the International System of measurement (SI) was established and some prefixes weren't used so much (e.g. nano).
For example, usually capacitors only used microfarad (sometimes written as \$MFD\$) and picofarad as units, this latter often written as micromicrofarad (\$\mu\mu F\$). Therefore \$10nF\$ could only be written as either \$10,000 pF\$ or \$0.01 \mu F\$.
Combine this with the need to encode other information on the smaller packages of the time (e.g. tolerance), and you end up with a metric ton of different encoding schemes, some more obscure than others.
Since old habits are hard to die, even in modern industry, the markings on the caps follow, in some way, the old tradition, where nanofarads "didn't exist".
Best Answer
Cost is the only real drawback. All the manf of lower esl packaged caps seem to want to charge you extra for the privilege. I've always assumed they had a meeting along the lines of "one of these caps replaces two regular ones so they must be double the price."
Plus if I recall they're not dramatically better. I could achieve a similar gain by going to 0201 or 0402 so why mess around with more expensive parts. If I want to be fancy I'll just use some idc parts :).
They're not bad for the values where say you can't get a 0402 or a 0201 but that starts to limit their useful range. But I think bang for your buck wise I would consider an x2y cap before bothering with 0306s much better value per real estate used.
I'd also add that there's much more to decoupling than just 1uF and 0.1uF so I usually prefer a wider range (.1, .22, .47, etc)