Craftspeople and artists work in or with (a particular material)** (OED)
It appears that 'in' ink became the normal usage around 1900. https://books.google.com/ngrams/graph?content=in+ink%2C+with+ink&year_start=1800&year_end=2000&corpus=15&smoothing=3&share=&direct_url=t1%3B%2Cin%20ink%3B%2Cc0%3B.t1%3B%2Cwith%20ink%3B%2Cc0
I can find no reference to support this, but for me there is a nuance that 'craft workers' work with a material whereas 'artists' work in a material (in suggesting a greater degree of 'knowing' the material and having creative vision for what it might be used to make).
1393 Gower Confessio Amantis (Fairf.) ii. l. 1850 (MED), To worche in latoun and in bras He lerneth for his sustienance.
?1473 Caxton tr. R. Le Fèvre Recuyell Hist. Troye (1894) I. lf. 26v, Than Iupiter began to lerne spynne and to werke in the silke.
1474 Caxton tr. Game & Playe of Chesse (1883) iii. iii. 93 Thise..ben named drapers..for so moche as they werke wyth wolle.
1538 T. Elyot Dict. Plasma, the warke of a potter, or of hym that worketh in erthe.
1539 Bible (Great) Isa. xix. 9 They that worke in flaxe.
1604 E. Grimeston tr. J. de Acosta Nat. & Morall Hist. Indies iv. vi. 223 The veine of Tinne..is..rough and very painfull to worke in.
1656 T. Blount Glossographia Configulate, to play the Potter, to work in clay.
1726 G. Leoni tr. L. B. Alberti Archit. III. 28 Those that work in wax, stuc or clay.
1759 R. Smith Harmonics (ed. 2) viii. 176 Any man who works true in brass may easily apply it [sc. this mechanism]..to any harpsichord ready made.
1825 J. Smith Mechanic (ed. 7) II. 288 It is simple and easy to cut a good screw. Any one, who works in metal, can make the tool.
1869 C. Boutell tr. J. P. Lacombe Arms & Armour ii. 38 The Greeks of that age..were able to temper it [sc. iron], and they had actually commenced working in it.
1979 Jrnl. Econ. Hist. 39 516 British prefabricators, whether working with wood, corrugated iron, or cast iron, had established the basic elements of industrialized building.
2002 M. Rendell Kings of Mountains (2003) i. 12 Exquisitely-skilled artisans working in wood, leather and bamboo-like guadua.