1/4" thick wood for under layment used for vinyl support tells you why it punctured and is likely to happen again in other areas with simple dropped items landing on protrusions. You have what you have now and a coarse patch made from wood splinters and sawdust mixed with a strong glue adhereing to filling the depression in the 1/4" wood to level original level is easy to do. After total dry/solid and scraped to smooth, glue the vinyl down and fill the crack with a close blended color waterproof filler that's around the 3 sides to prevent water protrusion and trapped rotting. Should be very hard to see the damage then.
If the damage is large enough or will leave and ugly scar, the ture laminate of Bamboo or other interlocking flooring would be a big improvement in strength and looks too and is just as easy to care for as vinyl. You have lots of choices as ways to fix it and have it professionally looking.
All I see is wallows in your present flat floor with age as the foam under the 1/4" wood will continus to depress with walking on it alone. It's a foam used as a support. A no no to me! Under a strong composite non-wood 1/4"+ sheet may be better but still far from strong as the only true supports are the floor stringers (joists) and they are spaced X apart!
