There are plenty of clues in the flavour text here to help us work out that this crossword's clues are all related to...
...Periodic Table elements. Notably, Sherlock's repeated references to his 'elementary' catchphrase, and Watson being a 'man of science'. Moreover, his surveying through the window of the properties outside reflects the fact that most clues contain references to properties (and uses) of the elements we are looking for. Lots of these rhyming clues also make use of elements (ho ho) commonly employed in cryptic crossword clues, like anagrams (marked in my explanations by '*'), hidden words ('_'), and reversals ('<').
The cryptic-type clues can be resolved as follows, each clue having an answer that begins with the same first letter as itself (property references presented in square brackets):
[Active in low friction stuff], it rhymes with ex's "not enough" (8) ANTIMONY = rhymes (in some accents) with 'ALIMONY'
[Best uses are in fibres spun, or obvious glass] turned up is one (5) BORON = (_N OR OB_)<
Coined Griphook when in German spelled, from the [horrid way it smelled] (6) COBALT = German 'KOBALT', from 'KOBOLD' (meaning 'goblin', e.g. Griphook from the Harry Potter series)
[Do wrap it up with no delays], tsutsumu in budo [decays] (7) DUBNIUM (highly radioactive) = (_MU IN BUD_)<
Excited in a TV show, I pour Emu a shot for [glow] (8) EUROPIUM = IPOUREMU*
Found when smelting iron flue, [in topaz with its lovely hue] (8) FLUORINE = IRONFLUE*
Gordian knotter's magic touch, turned out to be far too much (4) GOLD - a reference to the story of Midas, tie-er of the Gordian knot of Greek myth, later he of the 'golden touch'...
Heat or power plant takes advice to [use in fuel cell device] (8) HYDROGEN = HYDRO (Heat or power plant) + GEN (advice)
Its numbered set is often seen when I am driving to the green (4) IRON = a cryptic description of a set of 'iron' golf clubs...
Jot the name in western tongue of where nihonium was wrung (5) JAPAN = Nihonium is named after the country...
Kent can't return to fiction's place around red star in outer space (7) KRYPTON = a cryptic description of the planet Krypton, the fictional birthplace of Superman (a.k.a. Clark Kent), now destroyed and unable to be visited again...
[Long stopped using it in plumbing, brain effect is very numbing] (4) LEAD = a cryptic description of the properties and uses of lead...
Messenger brings me curry pot, [its liquid cool] but burning hot (7) MERCURY = lots going on here: definition for the Roman god Mercury (messenger of the gods), an anagram of MECURRY*, and references to the low boiling point of the element, and the surface temperature of the planet...
None elates me like this sign, an advert [with a brilliant shine] (4) NEON = an anagram of NONE*, plus reference to neon signs...
O Mum, is all my work a crib? [I really wrote it, with this nib] (6) OSMIUM = OMUMIS* (found in fountain pen nibs)
Pale blonde ain't plum she said, it's that, and [makes a lining for my cat] (8) PLATINUM = a pale blonde colour, anagram of AINTPLUM*, and used to line catalytic converters in vehicles...
Quirky term inspired by Joyce, off topic but my only choice (5) QUARK = not a chemical element, but an elementary particle, name inspired by a word in James Joyce's Finnegans Wake
[Rare and precious, quite top drawer,] needless use for humidor (7) RHODIUM = HUMIDOR*
Solid's best in fine utensil, very nice in [high class] pencil (6) SILVER = _SIL VER_
Taken from mutant Al Gore, [used in small capacitor] (8) TANTALUM = MUTANTAL*
Uttered by the hindu rani, [umph for heavy fissile sarnie] (7) URANIUM = _U RANI UM_
Valhalla's half are caked in blood, hers are baked in avian mud (8) VANADIUM = AVIANMUD*, with reference to Vanadis, another name for the Norse goddess Freyja, after whom the element is named...
Wise law form [fallen out of use, climate change is the excuse] (7) WOLFRAM = LAWFORM* NB 'Wolfram' is an old no-longer-used name for Tungsten;
[X-ray medium for detection], shows up in a non-exception (5) XENON = NONEX_<
Your aim is lost in immaturity, [making garnets of high purity] (7) YTTRIUM = (-im)M(-a)TURITY*
Zimbabwe mines some for [steel plating, batteries] don't have good rating (4) ZINC = references to its uses in steel plating and batteries.
Of course, Watson's quibbles lie with Sherlock's use of:
QUARK (an elementary particle, hence 'even more elementary') and JAPAN (a country), but he was always going to struggle with 'J', 'Q' and 'W' (for which he had to use an old name for an element), since no elements actually begin with those letters.
(Note the noticeably repeated use of the letters Q and J at the start of words in that section of the flavour text, to emphasise where Watson's disputes lie...)
Finally, here's how all the answers fit into the grid:
First place the ZINC-COBALT-LEAD-DUBNIUM-BORON-OSMIUM chain. Then XENON and EUROPIUM-PLATINUM. Next, continuing roughly clockwise, IRON-SILVER-VANADIUM-NEON-RHODIUM. Only FLUORINE can intersect with SILV[E]R, then we place QUARK, MERCURY, YTTRIUM, ANTIMONY and TANTALUM. There's only one place left for each of GOLD and JAPAN, before placing WOLFRAM, HYDROGEN, URANIUM and KRYPTON to finish.
